[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.
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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
More information about the gromacs.org_gmx-users