AMBER Archive (2007)

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

From: Chris Moth (chris.moth_at_vanderbilt.edu)
Date: Fri Nov 30 2007 - 08:11:40 CST


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/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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