[gmx-users] TIP4P water shrinks during energy minimization

David 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 
> this.
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.
> Valentin
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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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