[gmx-users] TIP4P water shrinks during energy minimization
v.gogonea at csuohio.edu
Sun Jun 5 01:38:52 CEST 2005
Thank you David for your suggestion. It worked.
On Jun 4, 2005, at 2:44 PM, David wrote:
> 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
>> 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
>> "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
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