AMBER Archive (2007)

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

From: Pavan G (pavanamber_at_gmail.com)
Date: Fri Nov 30 2007 - 10:35:02 CST

@Chris: Tried feeding raw trajectory to imin=5. Bizarre results.
Thanks for the link. I guess I'll try the restart method you suggested. Any
further suggestions are welcome.

Pavan Ghatty

On Nov 30, 2007 9:11 AM, Chris Moth <chris.moth_at_vanderbilt.edu> wrote:

> Perhaps you could use ptraj to create a restart format file for each of
> your trajectory frames, and get a better energy number with a one-step
> minimization (which just calculates the energy) on each of these.
>
> I am still curious though about your imin=5 result. If you do NOT alter
> the original trajectory in any way (don't wrap with ptraj), and just read
> it back in with imin=5, does that "help" at all?
>
> Finally, note that (documented elsewhere on the reflector) the energies
> reported by sander do not exactly correspond to the trajectory frame
> coordinates. This does not account for your graphs - but I wanted you to
> be aware of this as you get closer to a solution.
>
> See:
>
> http://structbio.vanderbilt.edu/archives/amber-archive/2007/1328.php
>
>
>
>
>
> > 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_at_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_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/>
> >> <http://compbio.ornl.gov/%7Epkc/plot.jpg>
> >> > sander-original.out
> >> > http://compbio.ornl.gov/~pkc/ <http://compbio.ornl.gov/%7Epkc/>
> >> <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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