[gmx-users] TIP4P water shrinks during energy minimization
spoel at xray.bmc.uu.se
Sat Jun 4 20:44:32 CEST 2005
On Sat, 2005-06-04 at 14:20 -0400, Valentin Gogonea wrote:
> Dear GMX Users:
> I am trying to perform energy minimization on a box of TIP4P water with
> a small organic molecule using OPLS force field. When I use the option
> -DFLEXIBLE the water seems to shrink and I get high forces. I used both
> "steep" and "l-bfgs" minimizers and got the same behavior. With "cg"
> minimizer the optimization crashes giving "nan" for coordinates.
> I may do something wrong here and I wonder if any of you experienced
check that the atoms are all excluded from the dummy when not using
constraints/settle. THis has been fixed in CVS.
> I included here the mdp file and a picture of the "optimized" box.
> Thank you for your help.
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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://xray.bmc.uu.se/~spoel
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