Re: Atomselect for coor, vel, xsc

From: Axel Kohlmeyer (
Date: Fri Nov 14 2014 - 09:02:47 CST

On Fri, Nov 14, 2014 at 9:58 AM, Josh Vermaas <> wrote:
> Not that I'm aware of, but you could use VMD to read in the coor and vel
> files, and then only write out the subset of atoms you are interested in (I
> think its $sel writenamdbin ...). The xsc file is a lost cause though. You
> are shrinking your box, so you'll need to write a new one that has the
> appropriate dimensions rather than the ones you started with.

not to mention that this kind of change will also require proper
equilibration, pretty much just like starting from scratch.

> On 11/13/2014 10:49 PM, Kevin C Chan wrote:
> Dear NAMD users,
> I have run quite a long simulation of a complex system and I do not want to
> "waste" it. I would like to continue the simulation with only part of my
> previous system. Does it exist any option of “atomselect" for the NAMD
> binaries (coor, vel, xsc) so I could use them for continuation?
> Thanks a lot,
> Kevin

Dr. Axel Kohlmeyer
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.

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