Notice that you will also need to generate a stripped down prmtop file
to analyze your results later with ptraj.
Cheers,
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 <jason.swails.gmail.com> 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 <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.
>>
>> 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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Received on Tue Jun 22 2010 - 13:30:07 PDT
