On Fri, Dec 17, 2010, Anindya Sarkar wrote:
>
> I have started MD simulation of two proteins with the AMBER package. But I
> have faced one problem during running of AMBER MD simulation. After the run
> of the first 5ns one, the coordinate files over 5000 trajectories were
> really big
It's unclear what you mean by "the coordinate files over 5000 trajectories".
What values are you using for ntwx, ntwv, ntwe? Typically, I would set
ntwx=2000 (or higher) and ntwv=ntwe=0 (since I don't want those files).
I usually set ntpr=ntwx, so I can see the energies at the same frequencies as
I have the coordinates, but this is just a personal preference.
How big the trajectory (-x) file is depends on the size of the system, the
frequency at which you dump coordinates, and the length of your simulation.
The longer you run a simulation, the less likely you are to need snapshots
at a short frequency. Hence, "typical" values of ntwx keep increasing as
computers become more powerful.
>
> Other thing is that I can not see the continuous increment of the output
> files during the run and I am getting only the files after the complete run.
You should be able to simply inspect the mdinfo file to see how things are
going, and how much time is left. If you "only get the files after the
complete run", that sounds like a quirk of your environment (or queuing
system); without knowing more information, it's hard to comment.
>
> I have another question that for coordinate files whether there are any
> differences among crd, inpcrd and mdcrd extensions and same for the
> parameter files also which are prmtop and parm7 ones. I am not sure which
> one I should use for the MD simulation runs.
The term "coordinate file" is indeed ambiguous, and there is no real standard
for file suffixes. The file types can be determined easily by examining them,
however. Two types of files contain coordinates.
1. restart files, specified by the -r parameter. I use .x as my
extension, but you should just pick something and stick with it.
The default name is "restrt".
2. trajectory files, specified by -x. I use .trj for this, but that is
just me. The default name is "mdcrd"
Unless you were using Amber before 2002, you probably have never seen an
"old-style" prmtop file. The current style is rather misleadingly called
"parm7" in VMD...it's probably time to see if they can update that.
>
> Thanks in advance.
> Anindya
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David A. Case | email:
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Chemistry & Chemical Biology | fax: +1-732-445-5958
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Received on Fri Dec 17 2010 - 12:00:04 PST
