Re: [GaMD-discuss] GaMD in Amber Suggestions
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Re: [GaMD-discuss] GaMD in Amber Suggestions
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From: Robyn S. <rs...@sk...> - 2017-10-25 17:10:26
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Hi Dr. Miao, Thanks for the help! Robyn ________________________________ From: Miao, Yinglong <mi...@ku...> Sent: Wednesday, October 25, 2017 10:35:24 AM To: Robyn Stix Cc: gam...@li... Subject: Re: GaMD in Amber Suggestions Hi Robyn, The anharmonicity can depend on the system size. It’s usually a small number around 1E-3 for my previous simulations. I also check standard deviation of the boost potential; it shall be less than 6 kcal/mol for most good reweighting calculations. Hope this helps, Yinglong Yinglong Miao, Ph.D. Assistant Professor Center for Computational Biology and Department of Molecular Biosciences University of Kansas http://miao.compbio.ku.edu On Oct 25, 2017, at 9:29 AM, Robyn Stix <rs...@sk...<mailto:rs...@sk...>> wrote: Hi Dr. Miao, Thank you! That makes a lot of sense. When running my simulations and reweighing I noticed that the anharmonicity for ntwx = 500 is approximately 10x greater than for ntwx = 50. I was wondering if the ntwx = 500 would get as low of an anharmonicity as the ntwx = 50 if it was run for 10 times as long. Also is there a specific cutoff in terms of anharmonicity where you can consider the reweighing good, and above that is considered not good? Thanks for all your help, Robyn ________________________________ From: Miao, Yinglong <mi...@ku...<mailto:mi...@ku...>> Sent: Wednesday, October 25, 2017 10:05:06 AM To: Robyn Stix Cc: gam...@li...<mailto:gam...@li...> Subject: Re: GaMD in Amber Suggestions Hi Robyn, I normally rename gamd.log to another like gamd-1.log, gamd-2.log, etc. after running each job. At the end you can combine them for reweighting … Yinglong Yinglong Miao, Ph.D. Assistant Professor Center for Computational Biology and Department of Molecular Biosciences University of Kansas http://miao.compbio.ku.edu<http://miao.compbio.ku.edu/> ======= For discussion on GaMD, please subscribe to mailing list: https://sourceforge.net/projects/gamd/lists/gamd-discuss, and send future emails to gam...@li...<mailto:gam...@li...>. ======= On Oct 25, 2017, at 9:02 AM, Robyn Stix <rs...@sk...<mailto:rs...@sk...>> wrote: Hi Dr. Miao, Thank you for all the help. I have one more question. With each subsequent production the gamd.log file is written over which makes it so the reweighing can only be done on the last production files. Is there a way to make each production add to the gamd.log file and not write over them? Thanks, Robyn ________________________________ From: Miao, Yinglong <mi...@ku...<mailto:mi...@ku...>> Sent: Friday, September 29, 2017 5:24:02 PM To: Robyn Stix Cc: gam...@li...<mailto:gam...@li...> Subject: Re: GaMD in Amber Suggestions Hi Robyn, Yes, you can still use the same scripts to reweight iE=2 GaMD simulations, and check the output anharmonicity and free energy profiles. By setting ntwx=50, you may indeed get too big simulation files. If you run iE=1 GaMD simulations for ~300 ns or longer, you may be able to set ntwx=500 (1ps) for reasonable reweighting. For iE=2, it might be hard for reweighting even with ntwx=50 so it doesn’t matter. All the best, Yinglong Miao, Ph.D. Assistant Professor Center for Computational Biology and Department of Molecular Biosciences University of Kansas 2030 Becker Drive, Suite 200D MRB Lawrence, KS 66047 mi...@ku...<mailto:mi...@ku...>; 785-864-8298 (office) http://miao.compbio.ku.edu<http://miao.compbio.ku.edu/> ======= For discussion on GaMD, please subscribe to mailing list: https://sourceforge.net/projects/gamd/lists/gamd-discuss, and send future emails to gam...@li...<mailto:gam...@li...>. ======= On Sep 29, 2017, at 8:12 AM, Robyn Stix <rs...@sk...<mailto:rs...@sk...>> wrote: Hi Dr. Miao, Thank you for all your suggestions. The k0P and k0D do reach 1.0 as output in the mdout file. I ended up having to change iE to 2 in the dual boost to see any isomerization in the omega bond of the proline residue. You mentioned that by changing iE to 2 the boost potential may get too high for accurate reweighting. I was wondering if the reweighting could still be done and anharmonicity could be used to determine the accuracy with iE = 2. I was also wondering if it is crucial for GaMD that ntwx = 50 and not a larger number as it causes the mdcrd file to take up a lot of space. Thank you for all your help, Robyn ________________________________ From: Miao, Yinglong <mi...@ku...<mailto:mi...@ku...>> Sent: Wednesday, September 13, 2017 8:09:49 PM To: Robyn Stix Cc: gam...@li...<mailto:gam...@li...> Subject: Re: GaMD in Amber Suggestions Hi Robyn, The input parameters for GaMD equilibration and production look fine to me. You can probably calculate the average and standard deviation for the boost potential (last two columns in gamd.log file) of the production part, and get an idea about the GaMD acceleration level. Also have the k0P and K0D reached 1.0 as output in the mdout file? Another option is to change iE=1 to iE=2 (upper bound for reference energy); the boost potential may get too high for accurate reweighing, but you can probably try it here to hopefully overcome your sampling problem … All the best, Yinglong Miao, Ph.D. Assistant Professor Center for Computational Biology and Department of Molecular Biosciences University of Kansas 2030 Becker Drive, Suite 200D MRB Lawrence, KS 66047 Phone: 785-864-8298 Email: mi...@ku...<mailto:mi...@ku...> https://compbio.ku.edu/yinglong-miao On Sep 13, 2017, at 9:33 AM, Robyn Stix <rs...@sk...<mailto:rs...@sk...>> wrote: Hi Dr. Miao, I attached the input files starting with the Gaussian equilibration as well as the restart files and the prmtop file for the dual boost I ran. Thank you so much, Robyn ________________________________ From: Miao, Yinglong <mi...@ku...<mailto:mi...@ku...>> Sent: Wednesday, September 13, 2017 10:17:38 AM To: Robyn Stix Cc: gam...@li...<mailto:gam...@li...> Subject: Re: GaMD in Amber Suggestions Hi Robyn, The GaMD acceleration greatly depends on sigma0D/sigma0P and the equilibration (nteb) parameters. Could you send me your input files, and I can possibly help you to take a look? All the best, Yinglong Miao, Ph.D. Assistant Professor Center for Computational Biology and Department of Molecular Biosciences University of Kansas 2030 Becker Drive, Suite 200D MRB Lawrence, KS 66047 Phone: 785-864-8298 Email: mi...@ku...<mailto:mi...@ku...> ======= For help on GaMD, please subscribe to the Gam...@li...<mailto:Gam...@li...> mailing list: https://sourceforge.net/projects/gamd/lists/gamd-discuss With that, feel free to post to the list in the future by sending emails to gam...@li...<mailto:gam...@li...>. ======= On Sep 13, 2017, at 7:33 AM, Robyn Stix <rs...@sk...<mailto:rs...@sk...>> wrote: Hi Dr. Miao, I am currently using GaMD in Amber to allow for proline to undergo isomerization from cis to trans for proline-rich intrinsically disordered proteins in research at Skidmore College. To first try out GaMD I did it on a tripeptide APA with two simulations, one with dual boost and one with just dihedral boost. I followed the template input files, besides changing it for their respective boosts and ran them for 50ns and found no proline trans-to-cis isomerization. I then doubled the boosts (to 12) in both and ran them for another 50ns to the same result. I was wondering if you had an suggestions as to how to manipulate the parameters of GaMD in Amber to allow for this isomerization to happen. Thanks for all your help, Robyn Stix '18 Chemistry, Biochemistry concentration Computer Science Minor Skidmore College rs...@sk...<mailto:rs...@sk...> <APA_eq2.rst><APA_eqGa.rst><APA_prod1_1.rst><APA_prod1_2.rst><APA_prod1_3.rst><APA_wat.prmtop><eqGa.in><prod_1_1.in><prod_1_2.in> |
