AMBER Archive (2007)

Subject: Re: AMBER: Re: Calculating Energies with imin=5

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Fri Nov 30 2007 - 06:32:04 CST

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_at_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>. 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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