[gmx-users] settle issue

Yang Ye leafyoung at yahoo.com
Tue Jul 29 09:44:12 CEST 2008

David van der Spoel wrote:
> 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.
Thanks, David. It works. With DispCorr=EnerPres, it gives 994.
>> Regards
>> Yuguang
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