[gmx-users] Energy conservation issue

Yang Ye leafyoung81-group at yahoo.com
Fri Oct 28 14:51:51 CEST 2005

Berk Hess wrote:

>> Reply-To: wu at hec.utah.edu,Discussion list for GROMACS users 
>> <gmx-users at gromacs.org>
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Subject: Re: [gmx-users] Energy conservation issue
>> Date: Thu, 27 Oct 2005 15:07:40 -0600
>> Thanks, Berk.
>> <snipped>
>> > I would say that the LJ cut-off is the largest source of errors.
>> > I don't know how DL_POLY handles this.
>> I checked its code; it is a simple truncation (without smoothing
>> whatsoever).
> From: Yujie Wu <yujie.wu at hec.utah.edu>
> I just ran your system in 3.3 for 1 ns.
> in single precision I get -70 kJ/mol drift
> in double precision I get +30 kJ/mol drift
> With a plain cut-off one of the biggest sources of error is the
> charge group based neighborlist.

Hi, Berk

A question from me: when define new residue, how shall I define the 
charge group? 1) group some atoms whose sum of charges is zero 2) just 
assign one charge group for each. Suppose that I use PME for calculation.
Yang Ye
/Computational Biology Lab
School of Biological Sciences
Nanyang Technological University
Tel: 6316-2884

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