[apbs-users] Manual calculation

 [apbs-users] Manual calculation From: Jesper Soerensen - 2012-05-23 20:48:28 Attachments: Message as HTML

Thread view

 [apbs-users] Manual calculation From: Jesper Soerensen - 2012-05-23 20:48:28 Attachments: Message as HTML
 Re: [apbs-users] Manual calculation From: Baker, Nathan - 2012-05-25 01:40:38 Attachments: Message as HTML ```Hello – You should use the same surface definition (surface type and probe radius) for all steps of the calculation. However, if the internal and external dielectric values are equal in some parts of the calculation, then the surface won’t actually be calculated for those parts of the calculation. Thanks, __________________________________________________ Nathan Baker Pacific Northwest National Laboratory Tel: +1-509-375-3997 http://nabaker.me; From: apbs-users@... [mailto:apbs-users@...] On Behalf Of Jesper Soerensen Sent: Wednesday, May 23, 2012 1:48 PM To: apbs-users@... Subject: [apbs-users] Manual calculation Dear all, I am running a manual (mg-manual) calculation with the SE surface. 3 calculations are solvated and 3 are dry like shown in the APBS examples and according to the thermodynamic cycle. My question is, in the dry set of calculations, should the 'srad' still be 1.4 like in the solvated calculations? I mean because in the absence of solvent does it make sense to define the SE surface? But at the same time changing it, results in two different surfaces being used and therefore some terms may not cancel out? I hope you can provide some insight. Best regards, Jesper ```
 Re: [apbs-users] Manual calculation From: Jesper Sørensen - 2012-05-25 18:58:32 Attachments: Message as HTML ```And so I am assuming that in the dry calculations, that the eps(in) and eps(ext) are equal, correct? In other words using a uniform dielectric constant. Best, Jesper On May 24, 2012, at 6:40 PM, Baker, Nathan wrote: > Hello – > > You should use the same surface definition (surface type and probe radius) for all steps of the calculation. However, if the internal and external dielectric values are equal in some parts of the calculation, then the surface won’t actually be calculated for those parts of the calculation. > > Thanks, > > __________________________________________________ > Nathan Baker > Pacific Northwest National Laboratory > Tel: +1-509-375-3997 > http://nabaker.me > > From: apbs-users@... [mailto:apbs-users@...] On Behalf Of Jesper Soerensen > Sent: Wednesday, May 23, 2012 1:48 PM > To: apbs-users@... > Subject: [apbs-users] Manual calculation > > Dear all, > > I am running a manual (mg-manual) calculation with the SE surface. > 3 calculations are solvated and 3 are dry like shown in the APBS examples and according to the thermodynamic cycle. > > My question is, in the dry set of calculations, should the 'srad' still be 1.4 like in the solvated calculations? > I mean because in the absence of solvent does it make sense to define the SE surface? But at the same time changing it, results in two different surfaces being used and therefore some terms may not cancel out? > > I hope you can provide some insight. > > Best regards, > Jesper > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/_______________________________________________ > apbs-users mailing list > apbs-users@... > https://lists.sourceforge.net/lists/listinfo/apbs-users ```
 Re: [apbs-users] Manual calculation From: Baker, Nathan - 2012-05-25 19:09:55 Attachments: Message as HTML ```Hi Jesper - Yes, a uniform dielectric is a pretty typical assumption for these kinds of calculations. Thanks, __________________________________________________ Nathan Baker Pacific Northwest National Laboratory Tel: +1-509-375-3997 http://nabaker.me; From: Jesper Sørensen [mailto:jesorensen@...] Sent: Friday, May 25, 2012 11:58 AM To: Baker, Nathan Cc: apbs-users@...; (apbs-users@...) Subject: Re: [apbs-users] Manual calculation And so I am assuming that in the dry calculations, that the eps(in) and eps(ext) are equal, correct? In other words using a uniform dielectric constant. Best, Jesper On May 24, 2012, at 6:40 PM, Baker, Nathan wrote: Hello - You should use the same surface definition (surface type and probe radius) for all steps of the calculation. However, if the internal and external dielectric values are equal in some parts of the calculation, then the surface won't actually be calculated for those parts of the calculation. Thanks, __________________________________________________ Nathan Baker Pacific Northwest National Laboratory Tel: +1-509-375-3997 http://nabaker.me; From: apbs-users@... [mailto:apbs-users@...] On Behalf Of Jesper Soerensen Sent: Wednesday, May 23, 2012 1:48 PM To: apbs-users@... Subject: [apbs-users] Manual calculation Dear all, I am running a manual (mg-manual) calculation with the SE surface. 3 calculations are solvated and 3 are dry like shown in the APBS examples and according to the thermodynamic cycle. My question is, in the dry set of calculations, should the 'srad' still be 1.4 like in the solvated calculations? I mean because in the absence of solvent does it make sense to define the SE surface? But at the same time changing it, results in two different surfaces being used and therefore some terms may not cancel out? I hope you can provide some insight. Best regards, Jesper ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/_______________________________________________ apbs-users mailing list apbs-users@... https://lists.sourceforge.net/lists/listinfo/apbs-users ```