Re: Writing number of atoms in a specific group to a file

From: Brian Radak (
Date: Fri Dec 16 2016 - 12:11:04 CST

The "measure" command might be useful for this, but I've never used it
from the NAMD interface myself.


On 12/16/2016 11:35 AM, Hamed Fadaei wrote:
> Dear NAMD users,
> I'm wondering if there's a way to calculate the number of atoms in a
> group and write it in a text file during a NAMD simulation. For
> example number of water molecules around a residue (So the selection
> also changes during time). I know I can do this as a processing with
> VMD but I need to stop the simulation at the moment this number
> reaches a certain value. Can you think of any possible way to do that?
> Best regards,
> Hamed

Brian Radak
Postdoctoral Appointee
Leadership Computing Facility
Argonne National Laboratory
9700 South Cass Avenue, Bldg. 240
Argonne, IL 60439-4854
(630) 252-8643

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