Bingwu Yu wrote:
> I did a short MD simulation. Then I use VMD to compare structure from rst
> file to output crd file. they are not the same. I assume the structure from
> rst file is the last frame of simulation.
No; it is determined by the ntwr parameter in your mdin input. This
tells SANDER or PMEMD how often to write a restart[1] file (restrt). The
top of the restart file will tell you at which time point it was
written, e.g. :
$ head restrt
46244 0.1200000E+03
19.1220675 57.0023318 63.2830587 19.0877594 56.1235335 62.7864259
18.1518750 57.2814583 63.3133342 19.4752553 56.8322566 64.2138824
19.9864352 58.0067683 62.6708065 19.7120218 58.0406612 61.6164572
.....etc.....
In the above example, there are 46,244 atoms in the system and the point
at which the coordinates and velocities were dumped was 120 ps into the
simulation.
> The structure from output crd file looks strange too. bond shows up between
> two non-related atoms . any idea?
If you are examining a restart file in VMD with a recent version of
AMBER (7 or later) you need to open it with:
vmd -parm7 prmtop -rst7 restrt
Regards,
Mark
Refs
=====
[1]
http://ambermd.org/formats.html#restart
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Received on Fri Mar 18 2011 - 10:30:04 PDT
