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
Received on Sun Mar 30 2014 - 20:00:02 PDT
