[gmx-users] Re: Re: Re: Electrostatics of Rigid Water

David van der Spoel spoel at xray.bmc.uu.se
Tue Aug 8 07:49:39 CEST 2006

Justin M. Shorb wrote:
> Greetings all!
> Thank you for your suggestions. I have figured out my problem with 
> getting different electrostatic forces from the same input file with 
> regards to flexible vs. rigid water. I wanted to post the results here 
> in case anyone in the future looks into the archives.
> The initial setup for settle is called before the MD loop begins, and 
> actually moves all the atoms a slight amount from the initial input 
> file. This small discrepancy accounted for my previous disagreement 
> between rigid and flexible water. Thus it was not the kernel that had 
> changed, but the positions of the atoms.

you can prevent this by setting the mdp option "unconstrained_start = yes"

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://folding.bmc.uu.se

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