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 <jason.swails.gmail.com>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.
>
> 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
>>
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue Jun 22 2010 - 10:30:06 PDT
