Hi Everybody,
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 and those are difficult for handling because I think those
contain the coordinate, velocity and energy informations. To get rid of this
problem, can anybody suggest me how I can generate the coordinate, velocity
and energy informations in separate files. I need only the trajectories in
the coordinate files. I am wondering if I give the output coordinate file
extension from crd to mdcrd whether it will help or not.
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.
Can anybody help me that I should include any particular command in the
execution file (having extension .in) and where it should be placed in the
file to see the file progressions during the MD runs.
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.
Thanks in advance.
Anindya
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Received on Fri Dec 17 2010 - 09:30:06 PST
