On Mon, May 18, 2015 at 10:13 AM, Juan Eiros Zamora <
j.eiros-zamora14.imperial.ac.uk> wrote:
> Hi all,
>
> I'm aware that even if I do exactly the same preparation of the system I
> will get differences on the results, as that is the nature of MD, but
> all in all the conclusions of the study should be the same.
>
> I would ask for the scripts but the issue is that they used NAMD instead
> of AMBER. Is there a way to use NAMD input files with AMBER? Or am I
> just being silly here?
>
NAMD has its own input format? I thought they just used either an Amber
topology file or a CHARMM PSF file with PAR/RTF/STR files? As for getting
Amber and NAMD to run with the same settings, see here:
http://ambermd.org/namd/namd_amber.html
I think they have their own coordinate format, but those are easy to
convert with any of a number of programs (e.g., VMD).
So if they used Amber files with NAMD, no conversion is necessary,
obviously. If they used CHARMM files, then you would need to use ParmEd's
"chamber" command to convert it to Amber-compatible format.
As others have said, simulation setup is not nearly as important as making
sure you don't introduce artifacts, the same overall potential parameters
and force fields are used for production, and all simulations are as
statistically converged as possible.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon May 18 2015 - 07:30:10 PDT
