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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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