[gmx-users] settle issue

David van der Spoel spoel at xray.bmc.uu.se
Mon Jul 28 20:26:57 CEST 2008

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 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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