[gmx-developers] More about the Ekin issue.
spoel at xray.bmc.uu.se
Mon Aug 15 20:49:40 CEST 2005
On Mon, 2005-08-15 at 18:17 +0200, Xavier Periole wrote:
> Berk Hess wrote:
> >> Ok, I sorted out the problems.
> >> 1) for the small system, the reaction-field was actually gone from
> >> the mdp file
> >> I used to run gmx33b. Using the tpr from gmx3.1 gives a difference of
> >> Epot
> >> but this time it is what one would expect from the difference of T.
> >> 2) for the big system the RF for excluded atoms was responsible.
> >> Again using
> >> the tpr from gmx3.1 give a difference but expected from the
> >> difference in T.
> >> I'd like to get more detail about this RF correction that is included
> >> (or excluded)
> >> in gmx33. could you be more precise ?
> > See the CVS manual and the CVS mdp_opt.html
> where can I find the CVS Manual ?
cvs co manual
> > BTW the CVS code also includes nice REMD code (in which I will fix the
> > NPT part today).
> I know about this version... and actually tried it. But I am used to
> another one where I can
> manipulate everything very easily !! Next project probably ... where
> would I find the analysis
> tools of REMD ??
What in particular are you thinking of? There is a new energy landscape
tool (g_sham) and we are working on a trajectory demultiplexing tool.
> > Berk.
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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 http://xray.bmc.uu.se/~spoel
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