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

From: Gustavo Seabra <>
Date: Tue, 22 Jun 2010 17:16:02 -0300

Notice that you will also need to generate a stripped down prmtop file
to analyze your results later with ptraj.

Gustavo Seabra
Professor Adjunto
Departamento de Química Fundamental
Universidade Federal de Pernambuco
Fone: +55-81-2126-7417

On Tue, Jun 22, 2010 at 2:09 PM, Jason Swails <> wrote:
> One thing I forgot to mention (though it's in the manual) -- this is only
> for the mdcrd (and probably mdvel if printed to) file, not the restart.
> All the best,
> Jason
> On Tue, Jun 22, 2010 at 1:08 PM, Jason Swails <>wrote:
>> 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.
>> 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
Received on Tue Jun 22 2010 - 13:30:07 PDT
Custom Search