Re: use of tiElecLambdaStart (NAMD 2.7b1)

From: Chris Harrison (char_at_ks.uiuc.edu)
Date: Fri Mar 27 2009 - 14:33:04 CDT

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: <51618.146.189.58.124.1238169651.squirrel_at_cmail.clarku.edu>
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> 	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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