[gmx-users] TIP4P water shrinks during energy minimization

[David]

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
> 
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
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
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++