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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--
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Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
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Received on Thu Mar 19 2015 - 20:00:03 PDT
