From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
Date: Fri Mar 27 2009 - 16:32:31 CDT
Just a little remark about what Chris wrote: setting tiElecLambdaStart
to 0 and tiVdwLambdaEnd to 1 will not remove the soft-core potential
(except if the vdwShift parameter is set to 0), but it will result in
"naked charges" at lambda close to 0 (resp. 1 for disappearing atoms),
which typically cause big-time numerical issues in the simulation.
On Fri, Mar 27, 2009 at 3:33 PM, Chris Harrison <char_at_ks.uiuc.edu> wrote:
> 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?
> 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: <51622.214.171.124.124.1238169651.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
>> 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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