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

From: Hamed Fadaei (hamed.fadaei111_at_gmail.com)
Date: Fri Dec 16 2016 - 12:52:06 CST

Actually I tried to see if there's any way to do it with TCL scripting in
NAMD but unfortunately I couldn't find anything related in NAMD user's
guide and tutorials for TCL scripting. Can you introduce any good source
for further readings?

On Fri, Dec 16, 2016 at 12:11 PM, Brian Radak <bradak_at_anl.gov> wrote:

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

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