Re: [AMBER] how to modify the code to save the trajectory of ONLY one part of atoms in .mdcrd file ?

From: Jason Swails <>
Date: Tue, 22 Jun 2010 13:08:11 -0400

See ntwprt variable in the amber manual. Only coordinates from atom number
1 to ntwprt are printed, so if your solute appears at the beginning of your
prmtop, and the solute is, say 3000 atoms, then setting ntwprt=3000 will
cause only the solute to be printed.

Hope this helps,

On Tue, Jun 22, 2010 at 12:16 PM, Dongshan Wei <> wrote:

> Hi All,
> I'm doing the explicit simulation of peptide folding in water, I need
> to save the trajectory in a high frequency (every ~0.2ps). If I save
> the trajectory of all atoms, the .mdcrd file will be very huge. So I
> just want to save the trajectory of ONLY the solute atoms (atoms of
> the peptide). Which command or which subroutine do I need to add or to
> modify?
> Thanks!
> Dongshan
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Tue Jun 22 2010 - 10:30:05 PDT
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