Thanks Dan.
I will give sander.MPI a try.
Just looked up mdout_analyzer.py (Thanks Jason .. glad that it is in
python!).
Best
Sandeep
On Thu, Mar 19, 2015 at 10:57 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Thu, Mar 19, 2015 at 2:00 PM, Sandeep Somani <ssomani.gmail.com> wrote:
> > 1. use ensemble keyword of cpptraj to extract trajectories for each
> > temperature
> > 2. process each trajectory via sander using imin=5
> > 3. grep out energy values from the generated mdout files
>
> Seems fine - by the way you can also read those mdout files directly
> into cpptraj or mdout_analyzer.py, so you may be able to skip the
> 'grep'.
>
> > This works, but the sander step is quite slow.
>
> If you've got access to a multi-core machine you should be able to use
> the MPI version of sander for some speedup here.
>
> > I think the same information can be extracted from the original mdout
> files
> > and rem.log file.
>
> Unfortunately no, not exactly. The integration scheme results in the
> energies and coordinates being offset by a timestep. The way that
> you're doing it is the best way to obtain the exact energies from your
> coordinates (especially for replica trajectories).
>
> >
> > Is there a cpptraj command for this?
>
> There will be a command in the upcoming cpptraj release, 'energy',
> which will allow the computation of simple energy terms (bond, angle,
> dihedral, vdw + electrostatic with no PBC) but for other energy terms
> (gb, PME nonbond) sander is still your best bet.
>
> -Dan
>
> > Or does anyone have a script to share? :-)
> >
> > Thanks in advance!
> >
> > Sandeep
> >
> > ---
> >
> > Sandeep Somani
> >
> > Discovery Sciences
> >
> > Janssen R&D
> >
> > Spring House PA
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>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
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>
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Received on Fri Mar 20 2015 - 05:00:02 PDT
