[gmx-users] Re: Re: energy decreasing in NVE simulation

Tsjerk Wassenaar tsjerkw at gmail.com
Thu May 20 13:14:00 CEST 2010

Hi Yun-an Yan,

In addition to the other things, COMM removal is also a source of
energy drift. It is better to center your solute afterwards.



On Thu, May 20, 2010 at 1:05 PM, Yan Yun-an <yun-an.yan at uni-rostock.de> wrote:
> Dear Erik,
> Thank you so much for your prompt reply. I appreciate it.
> Yun-an Yan
> Erik Marklund writes:
>>For more exotic NVE-systems I had to do some or several of the following
>>things to get stable Etot:
>>* have an even shorter timestep than one would expect from the applied
>>constraints and such.
> I will try a timestep with 0.5 fs.
>>* use double precision.
> The double precision is already in use.
>>* apply the constraints with lower tolerance/more iterations etc.
> I thought shake_tol = 1.e-8 is small enough. May I try an even smaller
> value?
> Or the lincs algorithm with lincs_order=8 and lincs_iter=2 is recommended
> instead of shake?
>>Then there's a few things I notice in your setup:
>>* I see that you do not use constrints at all. I would give it a shot.
> I will try.
>>* Why do you have two separate comm-grps?
> Since it is a solute-solvent fashion MD, I am trying to keeping the solute
> part close the center of the simulation box. But it does not work in this
> way.
> Do you have any idea about that?
>>Erik Marklund
>>Erik Marklund, PhD student
>>Dept. of Cell and Molecular Biology, Uppsala University.
>>Husargatan 3, Box 596,    75124 Uppsala, Sweden
>>phone:    +46 18 471 4537        fax: +46 18 511 755
>>erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/
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Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology
University of Groningen
The Netherlands

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