Re: generating xsc and vel files

From: Peter Freddolino (
Date: Mon Feb 02 2009 - 10:46:40 CST

Hi David,
the .xst file that namd writes contains the system dimensions at each
point where output is written; you should be able to just take the
appropriate timestep from it.
Unless you wrote a velocity dcd, there is no way to recover the
velocities at any particular point in time, but reassigning the
velocities to get you started should have a minimal effect on your system.

David A. Horita wrote:
> Hi,
> I've run an MD simulation but decided that I'd like to start another
> run from the middle of the previous run. I have the dcd and can pick
> an intermediate time point and generate starting coordinates for the
> second run; is there a way to regenerate the .xsc and .vel files for
> that particular time point? (I have the final .coor, .xsc, and .vel,
> but not the intermediate ones). I assume that I can always assign
> velocities based on a Gaussian distribution if necessary, but how
> about the .xsc? (The system is a water/protein/membrane with PME run
> NPTA. I could measure the approximate xyz dimensions, but if I had to
> do that, along with reassigning velocities, I suspect I'd need to
> reequilibrate, which is what I'm trying to avoid...)
> Thanks,
> David Horita
> -----------------------------
> David A. Horita, Ph.D.
> Department of Biochemistry
> Wake Forest University School of Medicine
> Winston-Salem, NC 27157-1016
> Tel: 336 713-4194
> Fax: 336 716-7671
> email: <>
> web:
> <>

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