[gmx-users] TIP4P water shrinks during energy minimization

[Valentin Gogonea]

Thank you David for your suggestion. It worked.

Valentin

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  
>> 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
> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 
> +
>
> _______________________________________________
> 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.
>