Hi,
On Sun, Mar 30, 2014 at 1:29 PM, Milo Westler <milo.nmrfam.wisc.edu> wrote:
> I am running back-to-back 10ns MD simulations (using pmemd.cuda). I want to
> use an arbitrary snapshot, chosen by me, from the just completed trajectory
> to be my restart file for the next 10ns run. Can I do this and if so how?
> I am using the Netcdf format for the trajectories.
>
You can extract a frame from a trajectory with cpptraj and use it as
initial coordinates for a new run, but unless you are recording velocities
as well as coordinates it will not be a "true" restart file. Depending on
what you want to do however, just the coordinates with new randomly
assigned velocities may be enough. Here are some examples of using cpptraj
to write a single coordinate frame (in this case frame 7) as a restart file:
# No velocity info, or combined coords/velocity netcdf traj file
parm topology.parm7
trajin traj.nc 7 7
trajout traj.7.rst7 restart
# Separate velocity traj file
parm topology.parm7
trajin traj.nc mdvel vel.nc 7 7
trajout traj.7.rst7 restart
Hope this helps,
-Dan
>
> Thanks,
>
> --
> -- Milo
> ===================================================
> National Magnetic Resonance Facility at Madison
> An NIH-Supported Resource Center
>
> W. Milo Westler, Ph.D.
>
> NMRFAM Director
> Senior Scientist
> and
> Adjunct Professor
> Department of Biochemistry
> University of Wisconsin-Madison
> 433 Babcock Drive
> Madison, WI USA 53706-1544
> EMAIL: milo.nmrfam.wisc.edu
> PHONE: (608)-263-9599
> FAX: (608)-263-1722
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
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http://home.chpc.utah.edu/~cheatham/
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Received on Sun Mar 30 2014 - 14:00:03 PDT
