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From: Thaer AlJadir <thaer.aljadir@po...>  20170213 17:01:48

Dear Seunghwan Baek, I had the same mistake before. I still believe there is a mistake in your force field files. I suggest to check the Torsion Style ,Torsion Coefficients, Angle Style and Angle Coefficients in your force field fie for each component. Then try to calculate the chemical potentials for each single component in one box NPT, it should give you in the output file as fallow Initial Energies for Box 1 Total molecules in this box 200 Molecules of type 1 : 200 total vibration 0.000 [K] 0.00000 [kcal/mol] regular 0.000 [K] 0.00000 [kcal/mol] bondbond(12) 0.000 [K] 0.00000 [kcal/mol] total angle 0.000 [K] 0.00000 [kcal/mol] regular 0.000 [K] 0.00000 [kcal/mol] angleangle 0.000 [K] 0.00000 [kcal/mol] total torsion 0.000 [K] 0.00000 [kcal/mol] regular 0.000 [K] 0.00000 [kcal/mol] improper 0.000 [K] 0.00000 [kcal/mol] total nonbond 0.009 [K] 0.00002 [kcal/mol] intramolecular 0.000 [K] 0.00000 [kcal/mol] 2body nonbond 0.000 [K] 0.00000 [kcal/mol] 3body nonbond 0.000 [K] 0.00000 [kcal/mol] tail correct. 0.009 [K] 0.00002 [kcal/mol] total coulombic 0.000 [K] 0.00000 [kcal/mol] real space 0.000 [K] 0.00000 [kcal/mol] intramolec. 0.000 [K] 0.00000 [kcal/mol] intermolec. 0.000 [K] 0.00000 [kcal/mol] self 0.000 [K] 0.00000 [kcal/mol] correction 0.000 [K] 0.00000 [kcal/mol] recip sum 0.000 [K] 0.00000 [kcal/mol] external field 0.000 [K] 0.00000 [kcal/mol] solvation 0.000 [K] 0.00000 [kcal/mol] total classical 0.00940678 [K] 0.0000186933 [kcal/mol] initial virial pressure in box 1 = 0.01 Best regards Thaer AlJadir PhD Student and Teaching assistant at the School of Chemical Engineering and Analytical Science  The University of Manchester  The Mill (B9)  Oxford Road  Manchester  M13 9PL  Tel: 07473889191 ________________________________ From: 백승환 <karw9ace@...> Sent: 07 February 2017 16:10:06 To: Thaer AlJadir; towheeusers@... Subject: Re: [Towheeusers] Chemical potential calculation with multicomponents Thank you for the email, AlJadir, I do not know there is a mistake in a force field. The "towhee_ff_TraPPEUA" is what I have used. I did not change anything in the file, of course. Even when I tried with only ndodencae, it resulted in the positive value of chemical potential. I attahced a part of my input file below. I would appreciate any comments for this. Best regards, inputformat 'Towhee' ensemble 'npt' temperature 353.0d0 pressure 3447.38d0 nmolty 7 nmolectyp 502 96 54 30 19 13 92 numboxes 1 stepstyle 'cycles' nstep 20000 printfreq 2000 blocksize 4000 moviefreq 4000 backupfreq 4000 runoutput 'full' pdb_output_freq 4000 pressure_virial_freq 10 trmaxdispfreq 40 volmaxdispfreq 40 chempotperstep 10 20 30 40 50 60 120 potentialstyle 'internal' ffnumber 1 ff_filename /location/towhee7.2.0/ForceFields/towhee_ff_TraPPEUA classical_potential 'LennardJones' classical_mixrule 'LorentzBerthelot' lshift .false. ltailc .true. rmin 1.0d0 rcut 13.8d0 rcutin 10.0d0 electrostatic_form 'none' linit F initboxtype 'dimensions' initstyle 'full cbmc' 'full cbmc' 'full cbmc' 'full cbmc' 'full cbmc' 'full cbmc' 'full cbmc' initlattice 'simple cubic' 'simple cubic' 'simple cubic' 'simple cubic' 'simple cubic' 'simple cubic' 'simple cubic' initmol 502 96 54 30 19 13 92 inix iniy iniz 10 10 10 hmatrix 80.0d0 0.0d0 0.0d0 0.0d0 80.0d0 0.0d0 0.0d0 0.0d0 80.0d0 pmvol 0.1d0 pmvlpr 1.0d0 rmvol 0.1d0 tavol 0.5d0 pm1boxcbswap 0.20d0 pm1cbswmt 0.14d0 0.28d0 0.42d0 0.56d0 0.70d0 0.84d0 1.0d0 pmcb 0.470d0 pmcbmt 0.0d0 0.16d0 0.32d0 0.49d0 0.66d0 0.83d0 1.0d0 pmall 0.0d0 0.16d0 0.32d0 0.49d0 0.66d0 0.83d0 0.99d0 pmtracm 0.735d0 pmtcmt 0.14d0 0.28d0 0.42d0 0.56d0 0.70d0 0.84d0 1.0d0 rmtrac 0.5d0 0.5d0 0.5d0 0.5d0 0.5d0 0.5d0 0.5d0 tatrac 0.5d0 pmrotate 1.0d0 pmromt 0.0d0 0.16d0 0.32d0 0.49d0 0.66d0 0.83d0 1.0d0 rmrot 0.05d0 0.10d0 0.15d0 0.15d0 0.15d0 0.30d0 0.30d0 tarot 0.5d0 cbmc_formulation 'Martin and Frischknecht 2006' cbmc_setting_style 'widom ideal' Original Message From: "Thaer AlJadir"<thaer.aljadir@...> To: "towheeusers@..."<towheeusers@...>; "백승환"<karw9ace@...>; Cc: Sent: 20170206 (월) 05:19:27 Subject: Re: [Towheeusers] Chemical potential calculation with multicomponents Dear Seunghwan Baek, I prefer to see your files ( input and force fields) to be more accurate in my answer. I believe there is a mistake in your force field files. I would suggest you to check it. Best regards Thaer AlJadir PhD Student and Teaching assistant at the School of Chemical Engineering and Analytical Science  The University of Manchester  The Mill (B9)  Oxford Road  Manchester  M13 9PL  Tel: 07473889191 ________________________________ From: 백승환 <karw9ace@...> Sent: 04 February 2017 03:34:29 To: towheeusers@... Subject: [Towheeusers] Chemical potential calculation with multicomponents Dear all, Hello, I am trying to calculate chemical potential for multicomponent molecules. I ran NPT for 10,000 cyles with 7 components having methane, ethane, propane, butane, pentane, hexane, and dodecane. The results are, u (Gibbs Total) K 1 1 4205.520 11.451 u (Gibbs Total) K 2 1 5189.762 40.365 u (Gibbs Total) K 3 1 4799.743 76.045 u (Gibbs Total) K 4 1 3745.663 196.951 u (Gibbs Total) K 5 1 2728.364 480.996 u (Gibbs Total) K 6 1 1632.444 214.713 u (Gibbs Total) K 7 1 6518.731 622.668 First, what does the positive value of the chemical potential mean? As far as I know, the chemical potential is negative. Shown in the manual, μtotal(i) = μresidual(i) + μdensity(i) + μisolation(i) μresidual(i) = μNpT Insertion(i)  μIsolation(i). Since there is no isolation, only μNpT Insertion(i) +μdensity(i) needs to be considered. μtotal(i) =  kB T ln[ < W * V / ( [N(i)+1] * Λ3(i) ) > ] μdensity(i) =  kB T ln[ < V / N(i) > / Λ3(i)) ] μNpT Insertion(i) =  kB T ln[ < V W > / < V > ] Secondly, I do not understand the following, μtotal(i) = μdensity(i) + μNpT Insertiona(i)  kB T ln[ < W * V / ( [N(i)+1] * Λ3(i) ) > ] =  kB T ln[ < V / N(i) > / Λ3(i)) ]  kB T ln[ < V W > / < V > ] =  kB T ln[< V / N(i) > / Λ3(i))*< V W > / < V >] <=> < W * V / ( [N(i)+1] * Λ3(i) ) > = < V / N(i) > / Λ3(i))*< V W > / < V > According to Martin and Siepmann 1998 (TCA)<http://towhee.sourceforge.net/references.html#martin_siepmann_1998_tca>;. The term W is <W+>/Wideal where W+ ‡and Wideal are the Rosenbluth weights of the ghost chain and of an ideal chain. Is this the weighted average insertion probability in Molecular Physics, 1990, 70, 6, 11451158, which is equation 6 in page 1150? Otherwise, how can I calculate this? Which source file I should refer to related to this? I see, as the number of carbon (length of the molecules) increases, the value of u (NpT Insertion) also increases. For example, u (Density) K 6 5886.576 u (NVT Insertion) K 6 4189.927 u (NpT Insertion) K 6 4189.927 u (Den. + NVT Insert) K 6 1696.649 u (Den. + NpT Insert) K 6 1696.649 u (Gibbs Total) K 6 1698.935 u (Density) K 7 5523.402 u (NVT Insertion) K 7 11449.852 u (NpT Insertion) K 7 11449.852 u (Den. + NVT Insert) K 7 5926.450 u (Den. + NpT Insert) K 7 5926.450 u (Gibbs Total) K 7 5419.709 I simply assume that the positive value of chemical potential of component7 comes from this large u (NpT Insertion). μNpT Insertion(i) =  kB T ln[ < V W > / < V > ] ln[ < V W > / < V > ] < 0 to get positive μNpT Insertion(i) then, [ < V W > / < V > ] < 1 In conclusion, the longer molecules may have smaller W. So I need additional explanation of this W, please. Moreover, the chemical potential deviation of my simulation is large. Give me suggestion for this and normally, how small they should be? I would appreciate your help! *A few days ago, I emailed with similar question as a nonmember. You are able not to post the email from this email address. Sorry for that. Seunghwan Baek [https://mail.naver.com/readReceipt/notify/?img=hw%2BCaB%2BZM6ndMq2YarkopAtwaAkCM6pCMxCop43oMqMZM4J4F4tqK4ElKoCgMX%2B0MoUl74lR74lcWNFlbX30WLloWrdQaX3cM6kZ74Jn76GCpz0ZtHITbX3Nb4Jv749CW4FcpBFdpBU5M6K5%2B6n%3D.gif] 
From: 백승환 <karw9ace@na...>  20170210 16:46:48

Dear Dr.Martin and all, I checked the chemical potential with several single component in bulk from hexane to octane. Hexane has the negative value of chemical potential and others have positive. In addition, one of example which is Gibbs_Ensemble/Catlow_Zeolite_4a was tested without any modification except the following. nstep 10000 printfreq 1000 blocksize 2000 moviefreq 2000 backupfreq 2000 pdb_output_freq 2000 pressure_virial_freq 20 trmaxdispfreq 20 volmaxdispfreq 20 I ran two times of this and the part of the result is, block averages Box: 1Block Energy Density Virial Press. Mol fracs 1 .25026693E+09 0.15432698E+01 0.00000000E+00 0.00956159 0.91791308 0.07252532 2 .25027411E+09 0.15434928E+01 0.00000000E+00 0.00955056 0.91685404 0.07359539 3 .25026832E+09 0.15431347E+01 0.00000000E+00 0.00956881 0.91860533 0.07182586 4 .25026236E+09 0.15431558E+01 0.00000000E+00 0.00956842 0.91856844 0.07186314 5 .25026588E+09 0.15431771E+01 0.00000000E+00 0.00956669 0.91840245 0.07203085Box: 2Block Energy Density Virial Press. Mol fracs 1 0.26058964E+06 0.61469957E03 0.96107534E+02 0.00000000 0.00000000 1.00000000 2 0.26021401E+06 0.60954490E03 0.94329221E+02 0.00000000 0.00000000 1.00000000 3 0.26077062E+06 0.61387740E03 0.94465403E+02 0.00000000 0.00000000 1.00000000 4 0.25989818E+06 0.61263514E03 0.96334977E+02 0.00000000 0.00000000 1.00000000 5 0.25971836E+06 0.61219609E03 0.95164311E+02 0.00000000 0.00000000 1.00000000Please see towhee_citations for a list of suggested citations for this simulation Block Averages ( 5 blocks) Units Type Box Average Standard Deviation u (Gibbs Total) K 3 1 5562.656 146.714u (Gibbs Total) K 3 2 5194.417 34.617u (NpT Insertion) K 3 1 9075.526 152.225u (NpT Insertion) K 3 2 9640.572 34.040u (NVT Insertion) K 3 1 9075.526 152.225u (NVT Insertion) K 3 2 9640.975 33.109 I wonder the meaning of the positive chemical potential, whether is an error or not.According to Theor Chem Acc 1998 99:347350, The chemical potential of heptane was all negative around 6000 K. Due to this, I guess mine has errors. Any help would be appreciated. Best regards, Seunghwan Baek 
From: 백승환 <karw9ace@na...>  20170207 16:11:57

Thank you for the email, AlJadir, I do not know there is a mistake in a force field. The "towhee_ff_TraPPEUA" is what I have used. I did not change anything in the file, of course. Even when I tried with only ndodencae, it resulted in the positive value of chemical potential. I attahced a part of my input file below. I would appreciate any comments for this. Best regards, inputformat 'Towhee' ensemble 'npt' temperature 353.0d0 pressure 3447.38d0 nmolty 7 nmolectyp 502 96 54 30 19 13 92 numboxes 1 stepstyle 'cycles' nstep 20000 printfreq 2000 blocksize 4000 moviefreq 4000 backupfreq 4000 runoutput 'full' pdb_output_freq 4000 pressure_virial_freq 10 trmaxdispfreq 40 volmaxdispfreq 40 chempotperstep 10 20 30 40 50 60 120 potentialstyle 'internal' ffnumber 1 ff_filename /location/towhee7.2.0/ForceFields/towhee_ff_TraPPEUA classical_potential 'LennardJones' classical_mixrule 'LorentzBerthelot' lshift .false. ltailc .true. rmin 1.0d0 rcut 13.8d0 rcutin 10.0d0 electrostatic_form 'none' linit F initboxtype 'dimensions' initstyle 'full cbmc' 'full cbmc' 'full cbmc' 'full cbmc' 'full cbmc' 'full cbmc' 'full cbmc' initlattice 'simple cubic' 'simple cubic' 'simple cubic' 'simple cubic' 'simple cubic' 'simple cubic' 'simple cubic' initmol 502 96 54 30 19 13 92 inix iniy iniz 10 10 10 hmatrix 80.0d0 0.0d0 0.0d0 0.0d0 80.0d0 0.0d0 0.0d0 0.0d0 80.0d0 pmvol 0.1d0 pmvlpr 1.0d0 rmvol 0.1d0 tavol 0.5d0 pm1boxcbswap 0.20d0 pm1cbswmt 0.14d0 0.28d0 0.42d0 0.56d0 0.70d0 0.84d0 1.0d0 pmcb 0.470d0 pmcbmt 0.0d0 0.16d0 0.32d0 0.49d0 0.66d0 0.83d0 1.0d0 pmall 0.0d0 0.16d0 0.32d0 0.49d0 0.66d0 0.83d0 0.99d0 pmtracm 0.735d0 pmtcmt 0.14d0 0.28d0 0.42d0 0.56d0 0.70d0 0.84d0 1.0d0 rmtrac 0.5d0 0.5d0 0.5d0 0.5d0 0.5d0 0.5d0 0.5d0 tatrac 0.5d0 pmrotate 1.0d0 pmromt 0.0d0 0.16d0 0.32d0 0.49d0 0.66d0 0.83d0 1.0d0 rmrot 0.05d0 0.10d0 0.15d0 0.15d0 0.15d0 0.30d0 0.30d0 tarot 0.5d0 cbmc_formulation 'Martin and Frischknecht 2006' cbmc_setting_style 'widom ideal' 
From: Fouad Oulebsir <fouad.oulebsir@un...>  20170206 16:09:23

Good morning to all, I would like to calculate the μisolation chemical potential in NVT ensemble for a pure fluid (methane) using pcff forcefield at a given pressure , i read the MCCCS TOWHEE (ALGORITHMS: CHEMICAL POTENTIAL) notice saying that we have to put NMOLECTYP=0. l did do that but I got error messages. I would be grateful if any one could help me. Thanks in advance. Fouad OULEBSIR Ph.D student University of Pau Southwest of France. 
From: Thaer AlJadir <thaer.aljadir@po...>  20170205 20:52:14

Dear Seunghwan Baek, I prefer to see your files ( input and force fields) to be more accurate in my answer. I believe there is a mistake in your force field files. I would suggest you to check it. Best regards Thaer AlJadir PhD Student and Teaching assistant at the School of Chemical Engineering and Analytical Science  The University of Manchester  The Mill (B9)  Oxford Road  Manchester  M13 9PL  Tel: 07473889191 ________________________________ From: 백승환 <karw9ace@...> Sent: 04 February 2017 03:34:29 To: towheeusers@... Subject: [Towheeusers] Chemical potential calculation with multicomponents Dear all, Hello, I am trying to calculate chemical potential for multicomponent molecules. I ran NPT for 10,000 cyles with 7 components having methane, ethane, propane, butane, pentane, hexane, and dodecane. The results are, u (Gibbs Total) K 1 1 4205.520 11.451 u (Gibbs Total) K 2 1 5189.762 40.365 u (Gibbs Total) K 3 1 4799.743 76.045 u (Gibbs Total) K 4 1 3745.663 196.951 u (Gibbs Total) K 5 1 2728.364 480.996 u (Gibbs Total) K 6 1 1632.444 214.713 u (Gibbs Total) K 7 1 6518.731 622.668 First, what does the positive value of the chemical potential mean? As far as I know, the chemical potential is negative. Shown in the manual, μtotal(i) = μresidual(i) + μdensity(i) + μisolation(i) μresidual(i) = μNpT Insertion(i)  μIsolation(i). Since there is no isolation, only μNpT Insertion(i) +μdensity(i) needs to be considered. μtotal(i) =  kB T ln[ < W * V / ( [N(i)+1] * Λ3(i) ) > ] μdensity(i) =  kB T ln[ < V / N(i) > / Λ3(i)) ] μNpT Insertion(i) =  kB T ln[ < V W > / < V > ] Secondly, I do not understand the following, μtotal(i) = μdensity(i) + μNpT Insertiona(i)  kB T ln[ < W * V / ( [N(i)+1] * Λ3(i) ) > ] =  kB T ln[ < V / N(i) > / Λ3(i)) ]  kB T ln[ < V W > / < V > ] =  kB T ln[< V / N(i) > / Λ3(i))*< V W > / < V >] <=> < W * V / ( [N(i)+1] * Λ3(i) ) > = < V / N(i) > / Λ3(i))*< V W > / < V > According to Martin and Siepmann 1998 (TCA)<http://towhee.sourceforge.net/references.html#martin_siepmann_1998_tca>;. The term W is <W+>/Wideal where W+ ‡and Wideal are the Rosenbluth weights of the ghost chain and of an ideal chain. Is this the weighted average insertion probability in Molecular Physics, 1990, 70, 6, 11451158, which is equation 6 in page 1150? Otherwise, how can I calculate this? Which source file I should refer to related to this? I see, as the number of carbon (length of the molecules) increases, the value of u (NpT Insertion) also increases. For example, u (Density) K 6 5886.576 u (NVT Insertion) K 6 4189.927 u (NpT Insertion) K 6 4189.927 u (Den. + NVT Insert) K 6 1696.649 u (Den. + NpT Insert) K 6 1696.649 u (Gibbs Total) K 6 1698.935 u (Density) K 7 5523.402 u (NVT Insertion) K 7 11449.852 u (NpT Insertion) K 7 11449.852 u (Den. + NVT Insert) K 7 5926.450 u (Den. + NpT Insert) K 7 5926.450 u (Gibbs Total) K 7 5419.709 I simply assume that the positive value of chemical potential of component7 comes from this large u (NpT Insertion). μNpT Insertion(i) =  kB T ln[ < V W > / < V > ] ln[ < V W > / < V > ] < 0 to get positive μNpT Insertion(i) then, [ < V W > / < V > ] < 1 In conclusion, the longer molecules may have smaller W. So I need additional explanation of this W, please. Moreover, the chemical potential deviation of my simulation is large. Give me suggestion for this and normally, how small they should be? I would appreciate your help! *A few days ago, I emailed with similar question as a nonmember. You are able not to post the email from this email address. Sorry for that. Seunghwan Baek [https://mail.naver.com/readReceipt/notify/?img=hPeCaB%2BZM6n9F6MYarkop4MdK6KXFxv9pzivKzEwpAioMxI0pxEXpxbmtzFXp6UwaLl5WLl51zlqDBFdp6d5MreRhoRdWX%2Bcp6ER%2BBF0bNFgWz0q%2BHK5bre9b4F0p4eZprE5W4kd.gif] 
From: 백승환 <karw9ace@na...>  20170204 03:34:40

Dear all, Hello, I am trying to calculate chemical potential for multicomponent molecules. I ran NPT for 10,000 cyles with 7 components having methane, ethane, propane, butane, pentane, hexane, and dodecane. The results are, u (Gibbs Total) K 1 1 4205.520 11.451 u (Gibbs Total) K 2 1 5189.762 40.365 u (Gibbs Total) K 3 1 4799.743 76.045 u (Gibbs Total) K 4 1 3745.663 196.951 u (Gibbs Total) K 5 1 2728.364 480.996 u (Gibbs Total) K 6 1 1632.444 214.713 u (Gibbs Total) K 7 1 6518.731 622.668 First, what does the positive value of the chemical potential mean? As far as I know, the chemical potential is negative. Shown in the manual, μtotal(i) = μresidual(i) + μdensity(i) + μisolation(i)μresidual(i) = μNpT Insertion(i)  μIsolation(i). Since there is no isolation, only μNpT Insertion(i) +μdensity(i) needs to be considered. μtotal(i) =  kB T ln[ < W * V / ( [N(i)+1] * Λ3(i) ) > ] μdensity(i) =  kB T ln[ < V / N(i) > / Λ3(i)) ]μNpT Insertion(i) =  kB T ln[ < V W > / < V > ] Secondly, I do not understand the following,μtotal(i) = μdensity(i) + μNpT Insertiona(i)  kB T ln[ < W * V / ( [N(i)+1] * Λ3(i) ) > ] =  kB T ln[ < V / N(i) > / Λ3(i)) ]  kB T ln[ < V W > / < V > ] =  kB T ln[< V / N(i) > / Λ3(i))*< V W > / < V >] <=> < W * V / ( [N(i)+1] * Λ3(i) ) > = < V / N(i) > / Λ3(i))*< V W > / < V > According to Martin and Siepmann 1998 (TCA).The term W is <W+>/Wideal where W+ and Wideal are the Rosenbluth weights of the ghost chain and of an ideal chain.Is this the weighted average insertion probability in Molecular Physics, 1990, 70, 6, 11451158, which is equation 6 in page 1150? Otherwise, how can I calculate this? Which source file I should refer to related to this? I see, as the number of carbon (length of the molecules) increases, the value of u (NpT Insertion) also increases. For example, u (Density) K 6 5886.576 u (NVT Insertion) K 6 4189.927 u (NpT Insertion) K 6 4189.927 u (Den. + NVT Insert) K 6 1696.649 u (Den. + NpT Insert) K 6 1696.649 u (Gibbs Total) K 6 1698.935 u (Density) K 7 5523.402 u (NVT Insertion) K 7 11449.852 u (NpT Insertion) K 7 11449.852 u (Den. + NVT Insert) K 7 5926.450 u (Den. + NpT Insert) K 7 5926.450 u (Gibbs Total) K 7 5419.709 I simply assume that the positive value of chemical potential of component7 comes from this large u (NpT Insertion). μNpT Insertion(i) =  kB T ln[ < V W > / < V > ]ln[ < V W > / < V > ] < 0 to get positive μNpT Insertion(i) then, [ < V W > / < V > ] < 1 In conclusion, the longer molecules may have smaller W. So I need additional explanation of this W, please.Moreover, the chemical potential deviation of my simulation is large. Give me suggestion for this and normally, how small they should be? I would appreciate your help! *A few days ago, I emailed with similar question as a nonmember. You are able not to post the email from this email address. Sorry for that. Seunghwan Baek 
From: Kaihang Shi <kshi3@nc...>  20160904 04:13:13

Dear Towhee users and developers, Recently I am modifying Towhee code for Ewald Sum in slab geometry. The only thing I have to do is to add a slab correction term, J = 2*pi/V*(∑q_i*z_i)^2, to the total coulombic energy, accounting for the contribution from image cells in z direction. pi is 3.14, V is volume of box, q_i and z_i are the charge and zcoordinate of atom i. I added three additional subroutines to account for this correction term, in energy_change.F file: twh_ec_slab: calculate energy change in slab correction term for chains in chainlist twh_ec_atomlist_slab: calculate energy change in slab correction term for atoms in atomlist in energy.F file: twh_ewald_slab: calculate the energy of slab correction term Accordingly, I've modified subroutines 'twh_engtotal' and 'twh_eng_print' in engtotal.F to include this slab correction term. I've also added this correction term in subroutines 'twh_energy_change' and 'twh_ec_atomlist_nonbond' in energy_change.F to account for the energy change with this slab correction term. I am testing my modified code right now, but some preliminary results are not good. So I was wondering if the modification I've done in Towhee is enough? I want this work for uvt ensemble and I was thinking if I forgot to change the corresponding codes in swap move part. Could any experienced users provide me with some guide on modifying code to serve my purpose? Any comment and advice will be appreciated. Thanks! Best regards, Kaihang 
From: Marcus Martin <marcus_martin@us...>  20160825 18:18:50

Howdy Towhee users, Version 7.2.0 of Towhee is now available. Unusually, some of the new variables in towhee_input do not currently do anything useful. I have been rebuilding the volume move routines in order to implement a periodic determination of the pressure via a ghost volume move, but this resulted in a surprising amount of changes being required throughout the code. Normally I would not release a version with knowingly unfinished features, but there have been numerous other bug fixes during this process that justify an early release. A lot of work was done on the configurationalbias routines with particular emphasis on cyclic molecules. Some problems with the MMFF94 force field implementation were resolved, and some issues with CBMC for cyclic molecules using class2 force fields were also fixed. Marcus  Marcus G. Martin 88 Martinez Road Edgewood NM 870158222 land (505) 286 4457 cell (505) 363 3179 http://www.photobirder.com towhee.sourceforge.net 
From: Marcus Martin <marcus_martin@us...>  20160824 18:02:47

From: HAdi Mokarizadeh <hadimokarizadeh@...> To: "towheeusers@..." <towheeusers@... > Cc: Date: Mon, 22 Aug 2016 12:55:02 +0000 (UTC) Subject: Error not a true bonded graph molecule Dear Towhee users I want to use NVT MC simulation for water molcules in zeolite. N_H2O=240 and T=298.0 Kelvin. In the input, type 2 is the H2O and type 1 is zeolite. when I run the input, I get the following error: "Molecule type 2 is not a true bonded graph molecule and has a nonzero move probability of 0.6700000000 for the com translation move". Could you please tell how i can solve this problem? and why this happens? I attached my files  The problem comes with how you have set up the input file for the water portion of your simulation. You did it as if all of the waters formed some gigantic superwater molecule that is not bonded together properly. You instead want to have a water molecule that is just the first 3 units of that description. Towhee uses that template for all 240 water molecules, you don't list them all together. Marcus  Marcus G. Martin 88 Martinez Road Edgewood NM 870158222 land (505) 286 4457 cell (505) 363 3179 http://www.photobirder.com towhee.sourceforge.net 
From: HAdi Mokarizadeh <hadimokarizadeh@ya...>  20160822 12:55:10

Dear Towhee users I want to use NVT MC simulation for water molcules in zeolite. N_H2O=240 and T=298.0 Kelvin. In the input, type 2 is the H2O and type 1 is zeolite. when I run the input, I get the following error:"Molecule type 2 is not a true bonded graph molecule and has a nonzero move probability of 0.6700000000 for the com translation move". Could you please tell how i can solve this problem? and why this happens?I attached my filesSincerelyHadi MokarizadehUniversity of Tehran 
From: HAdi Mokarizadeh <hadimokarizadeh@ya...>  20160812 17:35:16

Dear Towhee users I want to use NVT MC simulation for water molcules in zeolite. N_H2O=240 and T=298.0 Kelvin. In the input, type 2 is the H2O and type 1 is zeolite. when I run the input, I get the following error:"Molecule type 2 is not a true bonded graph molecule and has a nonzero move probability of 0.6700000000 for the com translation move". Could you please tell how i can solve this problem? and why this happens?I attached my filesSincerelyHadi MokarizadehUniversity of Tehran 
From: Marcus Martin <marcus_martin@us...>  20160804 19:06:15

On Mon, Aug 1, 2016 at 1:40 PM, Shenli Zhang <shlzhang@...> wrote: > Dear Towhee users, > > I use Towhee 7.1.0 version to study a yttria stabilized zirconia system > with 5416 atoms in total, and I wrote a script to do MC swap between > yttrium and zirconium, volume change and atom displacement under NPT > condition (P=100 kPa and T=1500). The interaction energy includes short > range exponential6 form and Coulomb interaction. I set the update of > volume and pressure calculation to be 100, with output frequency =10^5 > (total 10^7). However, I run for 1 day and a half and no block average > comes out. > > I'm quite uncertain if this is a normal speed? I'm also wondering if > anything goes on our cluster could make the calculation slow. > Answering that question depends on many details, but I think it is quite possible that this is a normal result. If you are doing the typical Monte Carlo cycles approach then 10^5 = 100,000 cycles is a pretty long simulation before an output and 10,000,000 cycles is very long. I would generally caution against going to such long simulations right from the start of a new project. The combination of time to equilibrate, and time to fix any human errors in the setup of the move probabilities and so forth means I like to perform many small simulations restarting from the previous output when I'm looking at a new system. Then you will also have a better feel for the time involved in a large production length simulation. Marcus  Marcus G. Martin 88 Martinez Road Edgewood NM 870158222 land (505) 286 4457 cell (505) 363 3179 http://www.photobirder.com towhee.sourceforge.net 
From: Shenli Zhang <shlzhang@uc...>  20160801 20:51:18

Dear Towhee users, I use Towhee 7.1.0 version to study a yttria stabilized zirconia system with 5416 atoms in total, and I wrote a script to do MC swap between yttrium and zirconium, volume change and atom displacement under NPT condition (P=100 kPa and T=1500). The interaction energy includes short range exponential6 form and Coulomb interaction. I set the update of volume and pressure calculation to be 100, with output frequency =10^5 (total 10^7). However, I run for 1 day and a half and no block average comes out. I'm quite uncertain if this is a normal speed? I'm also wondering if anything goes on our cluster could make the calculation slow. Thank you so much for your suggestions! Regards, Shenli 
From: Shenli Zhang <shlzhang@uc...>  20160801 19:41:03

Dear Towhee users, I use Towhee 7.1.0 version to study a yttria stabilized zirconia system with 5416 atoms in total, and I wrote a script to do MC swap between yttrium and zirconium, volume change and atom displacement under NPT condition (P=100 kPa and T=1500). The interaction energy includes short range exponential6 form and Coulomb interaction. I set the update of volume and pressure calculation to be 100, with output frequency =10^5 (total 10^7). However, I run for 1 day and a half and no block average comes out. I'm quite uncertain if this is a normal speed? I'm also wondering if anything goes on our cluster could make the calculation slow. Thank you so much for your suggestions! Regards, Shenli 
From: Thaer AlJadir <thaer.aljadir@po...>  20160716 00:35:44

Hello, I saw your input file and the chemical potential for water (#6423.985d0 #4226.760d0 5000.0d0) , I don't know which one is the chemical potential for water?. If you want to calculate the density at constant chemical potential then you should enter one value of chemical potential. Yes, average of specific density is the average overall steps . Is your system got equilibration? if not then it need to restart it. Please, read and follow the steps as it written here. Good luck. http://towhee.sourceforge.net/input/towhee_input_v7_0_x.html MCCCS Towhee (towhee_input Version 7.0.x)  SourceForge<http://towhee.sourceforge.net/input/towhee_input_v7_0_x.html>; towhee.sourceforge.net Overview. This section covers the variables that are set in the towhee_input file Version 7.0.x. Each variable is listed along with its type (logical, character ... Best regards Thaer AlJadir PhD Student and Teaching assistant at the School of Chemical Engineering and Analytical Science  The University of Manchester  The Mill (B9)  Oxford Road  Manchester  M13 9PL  Tel: 07473889191 ________________________________ From: Jungho Yang <ps.jhyang@...> Sent: 15 July 2016 00:41:21 To: towheeusers@... Subject: [Towheeusers] Calculate density Hi all, I am new to Towhee. I want to have chemical potential vs density using GCMC. My system is pure water (TIP3P) at 300 K. In this ensemble, I could calculate density at a constant mu. But I am not sure which density I should use. After simulation, there are averages and one of them is specific density. Is the specific density averaged over all steps or after converged? And Gibbs total chemical potential is not equal to the input chemical potential (5000). Why? I have also attached the final result and input. Kinds, Jay Averages Units Type Box 1 Volume nm^3 0.80000E+01 Volume^2 nm^6 0.64000E+02 Molecule Number 1 272.121 Molar Volume ml/mol 0.17704E+02 Specific Density g/ml 1.01755331 Number Density nm3 1 34.01510 Mole Fraction 1 0.9999960 Radius of Gyration A 1 0.3134096 Virial Pressure kPa 0.30299E+06 Virial S_xx kPa 0.31080E+06 Virial S_yy kPa 0.32080E+06 Virial S_zz kPa 0.33790E+06 Virial S_xy kPa 0.20097E+06 Virial S_xz kPa 0.17487E+06 Virial S_yz kPa 0.20679E+06 Virial P_tail kPa .20174E+05 Virial p_i <x_i><p_v> kPa 1 0.30299E+06 Ideal Pressure kPa 0.18791E+06 Ideal p_i <N/V>kT kPa 1 0.18791E+06 Total Classical K 0.1158E+07 Inter vdw K 0.1697E+06 Angle K 0.0000E+00 Torsion K 0.0000E+00 Intra vdw K 0.0000E+00 External Field K 0.0000E+00 Vibration K 0.0000E+00 Coulomb K 0.1327E+07 Tail vdw K 0.5844E+04 Solvation K 0.0000E+00 u (Density) K 1 3250.218 u (NVT Insertion) K 1 1563.311 u (NpT Insertion) K 1 1563.311 u (Den. + NVT Insert) K 1 4813.528 u (Den. + NpT Insert) K 1 4813.528 u (Gibbs Total) K 1 4871.754 G: Sum{<u_i><N_i>} kJ/mol 0.1102E+05 U kJ/mol 0.9624E+04 pV: <p><V> kJ/mol 0.1459E+04 H: <U> + <p><V> kJ/mol 0.8165E+04 H: <U + pV> kJ/mol 0.8170E+04 S: (<H>  <G>)/T kJ/K mol 0.7142E+01 Z: <p><V>/<N>RT 1.612435 
From: Jungho Yang <ps.jhyang@gm...>  20160714 23:41:29

Hi all, I am new to Towhee. I want to have chemical potential vs density using GCMC. My system is pure water (TIP3P) at 300 K. In this ensemble, I could calculate density at a constant mu. But I am not sure which density I should use. After simulation, there are averages and one of them is specific density. Is the specific density averaged over all steps or after converged? And Gibbs total chemical potential is not equal to the input chemical potential (5000). Why? I have also attached the final result and input. Kinds, Jay Averages Units Type Box 1 Volume nm^3 0.80000E+01 Volume^2 nm^6 0.64000E+02 Molecule Number 1 272.121 Molar Volume ml/mol 0.17704E+02 Specific Density g/ml 1.01755331 Number Density nm3 1 34.01510 Mole Fraction 1 0.9999960 Radius of Gyration A 1 0.3134096 Virial Pressure kPa 0.30299E+06 Virial S_xx kPa 0.31080E+06 Virial S_yy kPa 0.32080E+06 Virial S_zz kPa 0.33790E+06 Virial S_xy kPa 0.20097E+06 Virial S_xz kPa 0.17487E+06 Virial S_yz kPa 0.20679E+06 Virial P_tail kPa .20174E+05 Virial p_i <x_i><p_v> kPa 1 0.30299E+06 Ideal Pressure kPa 0.18791E+06 Ideal p_i <N/V>kT kPa 1 0.18791E+06 Total Classical K 0.1158E+07 Inter vdw K 0.1697E+06 Angle K 0.0000E+00 Torsion K 0.0000E+00 Intra vdw K 0.0000E+00 External Field K 0.0000E+00 Vibration K 0.0000E+00 Coulomb K 0.1327E+07 Tail vdw K 0.5844E+04 Solvation K 0.0000E+00 u (Density) K 1 3250.218 u (NVT Insertion) K 1 1563.311 u (NpT Insertion) K 1 1563.311 u (Den. + NVT Insert) K 1 4813.528 u (Den. + NpT Insert) K 1 4813.528 u (Gibbs Total) K 1 4871.754 G: Sum{<u_i><N_i>} kJ/mol 0.1102E+05 U kJ/mol 0.9624E+04 pV: <p><V> kJ/mol 0.1459E+04 H: <U> + <p><V> kJ/mol 0.8165E+04 H: <U + pV> kJ/mol 0.8170E+04 S: (<H>  <G>)/T kJ/K mol 0.7142E+01 Z: <p><V>/<N>RT 1.612435 
From: Pragati A Sharma <pa.sharma@nc...>  20160316 15:54:12

Dear all, I want to calculate solubility of CO2 in a polymer system. I have used OPLS forcefield for the polymer and prepared an equilibrated system using gromacs. I want to use the same forcefield and system in towhee. But I found out that for the same atomtypes of OPLS, towhee vibcoeff(1) values does not match with the bond constant values of opls in gromacs. For standard harmonic potential, vibcoeff(1) should be equal to "kb" values of gromacs opls ff. But it is not the same. e.g towhee: C CA bond coefficient 0.141900 (should denote bond length) 0.2360085854e+06 ( should denote bond constant, vibcoeff(1)) gromacs opls forcefield i j b kb C CA 0.14900 334720.0 If vibcoeff values in towhee are in kcal/mol and kb values in gromacs are in kj/mol. Still I could not get same values after conversion. ________________________________ Disclaimer: This message and the information contained herein is proprietary and confidential and subject to the policy statement of the National Chemical Laboratory, Pune, India. You may review the policy at http://www.nclindia.org/files/TermsAndConditions/WebmailDisclamer.aspx 
From: Shi, Jingbo <shijb@ma...>  20160130 06:44:09

Hi there, I got some hint on setting slit pore using hard walls separations from previous postings. However, the thickness of the hard walls increased the volume of the simulation box a lot if the slit pores are very narrow. Since the probability of accepted MC moves will be affected by the box volume, I worry we might get a systematic error here. Thank you in advance for sharing your thoughts. Regards, Jingbo Wood Science department University of British Columbia 
From: ho tuan <hoanhtuan1985@ya...>  20151117 23:04:51

Dear Towhee users and developers, I am Tuan Ho, from Sandia National Labs. I have a question regarding scaling the box in NPT simulation of aqueous solution. I am trying to study solubility of CO2 in NaCl solution. I used NPT with two boxes. First, I created a box of CO2 (box 2), and a box of NaCl+Water (box1). Then I equilibrated these two boxes to the right condition of temperature and pressure. For CO2 box it is very fast to scale the box to the right box volume corresponding to T, P. But for water+ NaCl box, it took me months. Anyone has experience on this simulation or know how to speed up the simulation please let me know. This is the probability I used in my simulation (I don't allow the swap between two boxes yet) pmvol 0.8d0 pmvlpr 0.9d0 1.0d0 rmvol 1.0d0 tavol 0.5d0 pm1boxcbswap 0.9d0 pm1cbswmt 0.2d0 0.0d0 0.6 1.0 pmtracm 0.950d0 pmtcmt 0.3d0 0.0 0.65 1.0d0 rmtrac 1.5d0 tatrac 0.8d0 pmrotate 1.0d0 pmromt 1.0d0 1.0d0 1.0 1.0 rmrot 0.05d0 tarot 0.5d0 Thank you very much. Tuan 
From: Pragati A Sharma <pa.sharma@nc...>  20151029 10:31:49

Hi, I want to calculate solubility of water in dodecane by GCMC calculations using towhee. I already have pdb file for equilibrated box of Dodecane containing 216 chains, generated using Gromacs code. I want to use the same pdb in towhee. So I converted pdb to towhee_coords, used initstyle='coords'. But the output pdb is generated for only 1 chain (nmolectyp =1 ). Why it is not taking coordinates for all the 216 chains (nmolectyp = 216) from towhee_coords and generating output pdb file. My Towhee_input file for GCMC calculation looks like: inputformat 'Towhee' ensemble 'uvt' temperature 300.0d0 nmolty 2 nmolectyp 216 1 chempot 0.0 730.0d0 numboxes 1 stepstyle 'moves' nstep 100 printfreq 10 blocksize 20 moviefreq 1000 backupfreq 1000'internal' ffnumber 1 ff_filename /data/home/psharma/montecarlo/towhee7.1.0/ForceFields/towhee_ff_Charmm27 classical_potential 'LennardJones' classical_mixrule 'LorentzBerthelot' lshift .false. ltailc .false. rmin 1.0d0 rcut 12.00d0 rcutin 5.0d0 electrostatic_form 'coulomb' coulombstyle 'ewald_fixed_kmax' kalp 5.6d0 kmax 5 dielect 1.0d0 linit T initboxtype 'dimensions' runoutput 'full' pdb_output_freq 100 pressurefreq 20 trmaxdispfreq 1000 volmaxdispfreq 1000 potentialstyle 'internal' ffnumber 1 ff_filename /towheebase/towhee7.1.0/ForceFields/towhee_ff_Charmm27 classical_potential 'LennardJones' classical_mixrule 'LorentzBerthelot' lshift .false. ltailc .false. rmin 1.0d0 rcut 12.00d0 rcutin 5.0d0 electrostatic_form 'coulomb' coulombstyle 'ewald_fixed_kmax' kalp 5.6d0 kmax 5 dielect 1.0d0 linit T initboxtype 'dimensions' initstyle 'coords' 'full cbmc' initlattice 'simple cubic' 'simple cubic' initmol 216 0 inix iniy iniz 6 6 6 hmatrix 43.2d0 0.0d0 0.0d0 0.0d0 43.2d0 0.0d0 0.0d0 0.0d0 43.2d0 pmuvtcbswap 0.25d0 pmuvtcbmt 0.0d0 1.0d0 pm1boxcbswap 0.0d0 pm1cbswmt 0.0d0 1.0d0 pmavb1 0.0d0 pmavb1in 0.5d0 pmavb1mt 1.0d0 1.0d0 pmavb1ct 1.0d0 1.0d0 1.0d0 1.0d0 avb1rad 5.0d0 pmavb2 0.0d0 pmavb2in 0.5 pmavb2mt 1.0d0 1.0d0 pmavb2ct 1.0d0 1.0d0 1.0d0 1.0d0 avb2rad 5.0d0 pmavb3 0.0d0 pmavb3mt 1.0d0 1.0d0 pmavb3ct 1.0d0 1.0d0 1.0d0 1.0d0 avb3rad 5.0d0 pmcb 0.50d0 pmcbmt 0.0d0 1.0d0 pmall 0.0d0 0.0d0 pmback 0.0d0 pmbkmt 0.0d0 1.0d0 pmpivot 0.0d0 pmpivmt 0.0d0 1.0d0 pmconrot 0.0d0 pmcrmt 0.0d0 1.0d0 pmcrback 0.0d0 pmcrbmt 0.0d0 1.0d0 pmplane 0.0d0 pmplanebox 1.0d0 planewidth 3.0d0 pmrow 0.0d0 pmrowbox 1.0d0 rowwidth 3.0d0 pmtraat 0.0d0 pmtamt 1.0d0 0.0d0 rmtraa 0.5d0 tatraa 0.5d0 pmtracm 0.75d0 pmtcmt 0.1d0 1.0d0 rmtrac 0.5d0 tatrac 0.5d0 pmrotate 1.0d0 pmromt 0.1d0 1.0d0 rmrot 0.05d0 tarot 0.5d0 cbmc_formulation 'Martin and Siepmann 1999 + Martin and Thompson 2004' cbmc_setting_style 'default ideal' #polymer input_style 'basic connectivity map' nunit 38 nmaxcbmc 38 lpdbnames F forcefield 'Charmm27' charge_assignment 'none' unit ntype 1 'CTL3' vibration 4 2 3 4 5 improper torsion 0 unit ntype 2 'HAL3' vibration 1 1improper torsion 0 unit ntype 4 'HAL3' vibration 1 1 improper torsion 0 unit ntype 5 'CTL2' vibration 4 1 6 7 8 improper torsion 0 unit ntype 6 'HAL2' vibration 1 5 improper torsion 0 unit ntype 7 'HAL2' vibration 1 5 improper torsion 0 unit ntype 8 'CTL2' vibration 4 5 9 10 11 improper torsion 0 unit ntype 9 'HAL2' vibration 1 8 improper torsion 0 unit ntype 10 'HAL2' vibration 1 8 improper torsion 0 unit ntype 11 'CTL2' vibration 4 8 12 13 14 improper torsion 0 unit ntype 12 'HAL2' vibration 1 11 improper torsion 0 unit ntype 13 'HAL2' vibration 1 11 improper torsion 0 unit ntype 14 'CTL2' vibration 4 11 15 16 17 improper torsion 0 unit ntype 15 'HAL2' vibration 1 14 improper torsion 0 unit ntype 16 'HAL2' vibration 1 14 improper torsion 0 unit ntype 17 'CTL2' vibration 4 14 18 19 20 improper torsion 0 unit ntype 18 'HAL2' vibration 1 17 improper torsion 0 unit ntype 19 'HAL2' vibration 1 17 improper torsion 0 unit ntype 20 'CTL2' vibration 4 17 21 22 23 improper torsion 0 unit ntype 21 'HAL2' vibration 1 20 improper torsion 0 unit ntype 22 'HAL2' vibration 1 20 improper torsion 0 unit ntype 23 'CTL2' vibration 4 20 24 25 26 improper torsion 0 unit ntype 24 'HAL2' vibration 1 23 improper torsion 0 unit ntype 25 'HAL2' vibration 1 23 improper torsion 0 unit ntype 26 'CTL2' vibration 4 23 27 28 29 improper torsion 0 unit ntype 27 'HAL2' vibration 1 26 improper torsion 0 unit ntype 28 'HAL2' vibration 1 26 improper torsion 0 unit ntype 29 'CTL2' vibration 4 26 30 31 32 improper torsion 0 unit ntype 30 'HAL2' vibration 1 29 improper torsion 0 unit ntype 31 'HAL2' vibration 1 29 improper torsion 0 unit ntype 32 'CTL2' vibration 4 29 33 34 35 improper torsion 0 unit ntype 33 'HAL2' vibration 1 32 improper torsion 0 unit ntype 34 'HAL2' vibration 1 32 improper torsion 0 unit ntype 35 'CTL3' vibration 4 32 36 37 38 improper torsion 0 unit ntype 36 'HAL3' vibration 1 35 improper torsion 0 unit ntype 37 'HAL3' vibration 1 35 improper torsion 0 unit ntype 38 'HAL3' vibration 1 35 improper torsion 0 #water input_style 'basic connectivity map' nunit 3 nmaxcbmc 3 lpdbnames F forcefield 'Charmm27' charge_assignment 'none' unit ntype 1 'HT' vibration 1 2 improper 0 unit ntype 2 'OT' vibration 2 1 3 improper 0 unit ntype 3 'HT' vibration 1 2 improper 0 Can anybody help me out, how to solve this problem. Thanks ________________________________ Disclaimer: This message and the information contained herein is proprietary and confidential and subject to the policy statement of the National Chemical Laboratory, Pune, India. You may review the policy at http://www.nclindia.org/files/TermsAndConditions/WebmailDisclamer.aspx 
From: Chandan Choudhury <iitdckc@gm...>  20150724 15:02:54

Dear Towhee users, I have just started using Towhee and trying out the examples. Can someone point me how do I view the simulation trajectories (towhee_movie) for NPT and uVT ensembles. Thanks Chandan  Chandan Kumar Choudhury National Chemical Laboratory, Pune India *"All work and no play makes Jack a dull boy...”* 
From: <doerrstein@po...>  20150604 19:17:23

Dear towheeusers, dear Marcus, I'm quite new to towhee and have problems with Cylopentane in the NpTensemble. I want to use the TrappeUA Potential with paramters taken from the Siepman page (http://www.chem.umn.edu/groups/siepmann/trappe/molname.php). Since I didn't find the parameters in the regular towhee_ff_TraPPEUA file, I created a forcefield file on my own. Unfortunately I get the following error, when I start the simulation: INITCONF: building template for molecule type: 1 Initial Structure Growth Trial: 1 unable to generate an initial conformation molecule type 1 READTOWHEE: there was an error in initconf I attached my input and force field file ( called ff). I would be very happy, if anybody could give me some advice. Thank you very much for your effort in advance. Best regards Mark 
From: Maytham Al Ismail <maytham@st...>  20150514 11:08:30

Dear all, I'm conducting molecular simulations to determine VLE for methane inside graphitic slit pores. The ensemble is nvt with 2 boxes. Each box is a slit pore. How can I perform a volume exchange between the two boxes anisotropically? For example, if I change hmatrix in xdirection of one box by let's say +1 angstrom, I want to change the same hmatrix (i.e. in xdirection) of the other box by 1 angstrom. pmcell is used for anisotropic volume move. However, the volume of one box is changed anisotropically, but the volume of the second box is changed isotropically. Is there a way to ask the molecular simulator to conduct anisotropic volume changes for both boxes? Thank you, Maytham 
From: Jianying Hu <jxh546@ca...>  20150410 19:14:22

Dear Friends, Recently I am learning Towhee and have some questions: 1) I have PDB file of a molecule. Can I use pdb file directly or need I convert pdb to towhee_coords file? And how to convert? 2) For invib, do I need to list all atoms following the pdb file? Or I only list different types of atoms? 3) For ijvib, I did not figure out the meaning of each number? 4) In the examples, I saw 'd0' in some items, like 'kalp 5.6d0'. I thought the unit is Angstrom. 5) How to consider a system containing different molecules? 6) Finally, in my system, there is no solvent. What value should be for 'dielect'? Thank you so much in advance! Jane Case Western Reserve University 2104 Adelbert RD, Bingham Building 203C Cleveland, OH 44106 Email: jxh546@... 
From: Salomon Turgman Cohen <sturgman@gm...>  20150205 20:22:17

Hey Marcus, I want to perform simulations of the model described in this paper: http://pubs.acs.org/doi/abs/10.1021/ma902081m I remember in my previous work with towhee that it had issues if there where rings within a molecule's topology. Will towhee be able to work with such a model with 2D bond connectivity? s  Salomon Turgman Cohen Assistant Professor Chemical Engineering Kettering University (919) 3419650 