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,
Jason
On Tue, Jun 22, 2010 at 12:16 PM, Dongshan Wei <dswei0523.gmail.com> 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
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jun 22 2010 - 10:30:05 PDT
