Re: non-zero charge

From: Chris Harrison (
Date: Wed Jan 19 2011 - 21:08:22 CST

Dear Joyce,

NAMD's PME has a "neutralizing plasma" coded to prevent propogation of charges
across periodic replicas. However, leaving a charge, and more so a non-integer
charge, when otherwise avoidable is considered poor practice and can lead to
possible artifacts or, in some pathological cases, issues with the
PME grid.

More importantly for your case, you should properly re-parameterize
residue charges using electrostatic fitting procedures. Poorly fitted
charges can lead to significant simulation artifacts ranging from PME
crashes to incorrect dynamics results that aren't easily detected and in
worst cases even published.

An overview of the parameter fitting procedure, and related papers, can
be found in:
MacKerell, A.D., Jr. "Atomistic Models and Force Fields" in
Computational Biochemistry and Biophysics, O.M. Becker, A.D. MacKerell,
Jr., B. Roux and M.Watanabe, Eds., Marcel Dekker, Inc. New York, 2001,
p. 7-38


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                          Voice: 217-244-1733              Fax:   217-244-6078
Kwee Hong <> writes:
> Date: Thu, 20 Jan 2011 00:17:45 +0800
> From: Kwee Hong <>
> To: namd-l <>
> Subject: namd-l: non-zero charge
> Hi all,
> I'm simulating a protein where its CYS is deprotonated and bound to Zn2+.
> I did some modification to the topology file. After the modification, CYS'
> charge is -0.8 while Zn2+ has a charge of 1.2.
> When I evaluate my system charge with the command below:
> set sel [atomselect top all]
> eval vecadd [$sel get charge]
> The charge of my sys tem is -0.39999932795763016.
> I wana run my system in PME. So, is there any way I can neutralize my
> system? Or it's ok for me to proceed to the simulation without neutralizing
> my system?
> All suggestion are welcomed.
> Thanks.
> Regards,
> Joyce

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