[gmx-users] settle issue

[Mu Yuguang (Dr)]

Thanks David,
To switch on Dispersion Correction to the pressure will work !

Regards
Yuguang
 
Assist. Prof. Dr. Yuguang Mu
School of Biological Sciences
60 Nanyang Drive 
Nanyang Technological Uiversity
Singapore
Tel: +65-63162885
email:ygmuATntu.edu.sg
http://www.sbs.ntu.edu.sg/Staff/YGMu/index.php
-----Original Message-----
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of David van der Spoel
Sent: Tuesday, July 29, 2008 2:27 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] settle issue

Mu Yuguang (Dr) wrote:
> Dear All,
> When I try to simulate TIP4Pew water box at 298K, and found the
density
> got from gromacs is relative low (983 g/cm3) than the amber (sander)
> version 994 g/cm3. I cannot find the reason. The parameters for the
> tip4pew model are identical. When I check some intra-molecular
> distances, and seem to find a hint: in gromacs simulation the
> intra-molecular atom-atom distance (should be fixed by settle)
> fluctuation is quite large!
> How can one increase the accuracy of settles in gromacs? 
> 
Settle is analytical and there is no tolerance. However you may be using

settle with the SPC parameters (unlikely though). Maybe you should turn 
on the Dispersion Correction to the pressure (EnerPres). That gives a 
similar density difference.


> Regards
> Yuguang
>  
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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