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.
________________________________________________________________________
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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