Thanks, I'll give it a try.
On Sun, Mar 30, 2014 at 9:30 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> On Sun, Mar 30, 2014 at 4:27 PM, Milo Westler <milo.nmrfam.wisc.edu>
> wrote:
>
> > I assume the velocity entries are vectors, correct?
> >
>
> Yes, velocity trajectories contain the X, Y, and Z components of the
> velocity vector for each atom in units of Angstroms / 1/20.455 ps (the
> 1/20.455 factor has to do with unit conversion as Amber uses lengths in
> Angstroms, masses in amu, and energies in kcal/mol).
>
> -Dan
>
>
> >
> >
> > 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
> > > >
> =======================================================================
> > > > ========
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > >
> > >
> > >
> > > --
> > > -------------------------
> > > 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/
> > > (801) 587-9652
> > > (801) 585-6208 (Fax)
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > -- 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
> > =======================================================================
> > ========
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> -------------------------
> 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/
> (801) 587-9652
> (801) 585-6208 (Fax)
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-- 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 Mon Mar 31 2014 - 06:30:03 PDT
