From: Chris Harrison (char_at_ks.uiuc.edu)
Date: Fri Mar 27 2009 - 15:45:41 CDT
After re-reading my earlier email I think my wording may cause potentially unnecessary concern from you. While analytically it is desirable to have a neutral charge in PME, the implementation in NAMD effectively neutralizes forces resulting from the "infinite propagation" of charge. We can discuss how in more detail if necessary, but this does permit for example such perturbations as Leu -> Lys within a given simulation run. I probably should have said "While not balancing the charge may yield reasonable or correct results, the analytical propogation of an infinite charge in PME is generally felt to be bad form." The key being the difference between an "analytical" treatment and as treated in the implementation in NAMD. If you can easily do a perturbation and maintain net neutral charge without introducing additional complexity or degrees of freedom, then it's probably a good idea to do it; however in biological systems it is often debatable if this can be done easily without complicating things.
-- Chris Harrison, Ph.D. Theoretical and Computational Biophysics Group NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801 char_at_ks.uiuc.edu Voice: 217-244-1733 http://www.ks.uiuc.edu/~char Fax: 217-244-6078 Chris Harrison <char_at_ks.uiuc.edu> writes: > From: Chris Harrison <char_at_ks.uiuc.edu> > Date: Fri, 27 Mar 2009 14:33:04 -0500 > To: brmorgan_at_clarku.edu > Cc: namd-l_at_ks.uiuc.edu > Subject: Re: namd-l: use of tiElecLambdaStart (NAMD 2.7b1) > Return-Path: charris5_at_gmail.com > Message-ID: <20090327193303.GG90447_at_tcbdhcpbi-142.beckman.uiuc.edu> > > Brittany, > > Can you explain why you can't use a perturbation that maintains > neutrality? While not balancing the charges may not lead to problems, > it is in general very bad form as you'll essentially be propogating to > an infinite charge via PME periodicity. > > The default value is 0.5. Using a zero value with tiElecLambdaStart and a tiVdwLambdaEnd value of 1 will essentially remove the soft-core potential. Unless there is a specific reason to change tiElecLambdaStart it's probably best to leave it at its default of 0.5 .... is there a reason you want to change it? > > C. > > > > -- > Chris Harrison, Ph.D. > Theoretical and Computational Biophysics Group > NIH Resource for Macromolecular Modeling and Bioinformatics > Beckman Institute for Advanced Science and Technology > University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801 > > char_at_ks.uiuc.edu Voice: 217-244-1733 > http://www.ks.uiuc.edu/~char Fax: 217-244-6078 > > > brmorgan_at_clarku.edu writes: > > From: brmorgan_at_clarku.edu > > Date: Fri, 27 Mar 2009 12:00:51 -0400 (EDT) > > To: namd-l_at_ks.uiuc.edu > > Subject: namd-l: use of tiElecLambdaStart (NAMD 2.7b1) > > Return-Path: char_at_halifax.ks.uiuc.edu > > Message-ID: <516184.108.40.206.124.1238169651.squirrel_at_cmail.clarku.edu> > > X-Spam-Status: No, score=-0.5 required=5.0 tests=AWL,BAYES_00,NO_REAL_NAME > > autolearn=no version=3.1.7-0+tcb1 > > > > Hi, > > > > In the thermodynamic integration implemented in NAMD 2.7b1, should > > tiElecLambdaStart always be used, and how would one determine the best > > value to use? How much does the use of a non-zero tiElecLambdaStart affect > > the results? My system changes in total charge as a function of lambda and > > I plan to use PME. > > > > Thank you, > > Brittany Morgan > >
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