I assume the velocity entries are vectors, correct?
On Sun, Mar 30, 2014 at 3:42 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
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--
-- 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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Received on Sun Mar 30 2014 - 16:30:03 PDT
