The water simulation was just a test. I have other simulations with only a
trajectory for which I would like to calculate the energies. I should admit
that I lost the log/out files sander wrote during the runs. Any suggestions?
Pavan Ghatty
On Nov 30, 2007 7:32 AM, Carlos Simmerling <carlos.simmerling.gmail.com>
wrote:
> there seems to be a problem with recalculation of NPT trajectories with
> sander.
> the box is read in but seems to be ignored by the PME setup.
> imin=5 is usually for MM-PBSA type calculations where water has been
> stripped. for now you should use your sander energies.
>
>
> On Nov 30, 2007 7:24 AM, Pavan G <pavanamber.gmail.com> wrote:
>
> > Hello All,
> >
> > >
> > > I heated water from 50 to 200K in a 100ps long simulation in a NPT
> > > ensemble. I then used ptraj to process the raw trajectory(1) ensuring that
> > > the output was in a periodic box(2). I then used
> > > ---------------
> > > test sander
> > > &cntrl
> > > imin = 5,
> > > maxcyc = 1,
> > > ntpr = 1,
> > > ntwx=1,
> > > /
> > > ------------------
> > > to get energies using sander and the imaged trajectory(2). Both
> > > original and imin=5 output files are here:
> >
> > http://compbio.ornl.gov/~pkc/ <http://compbio.ornl.gov/%7Epkc/plot.jpg>
> > sander-original.out
> > http://compbio.ornl.gov/~pkc/ <http://compbio.ornl.gov/%7Epkc/plot.jpg>
> > sander-imin-5.out
> >
> > > The energies looked like this http://compbio.ornl.gov/~pkc/plot.jpg<http://compbio.ornl.gov/%7Epkc/plot.jpg>. Could somebody comment on the discrepancy? For those who cannot access the
> > > figure, the sander-original energy data reaches -3700 Kcal/mol while the
> > > data from imin=5 reached -3300 Kcal/mol.
> > >
> > > Thanks
> > > Pavan Ghatty
> > >
> >
> >
>
>
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Received on Sun Dec 02 2007 - 06:07:34 PST
