Hi Marek,
On 14/9/2010, at 11:32 a.m., Marek Maly wrote:
> Dear all,
>
> is there any way how to obtain, for the given frame from amber MD
> trajectory, list of chosen atoms with associated
> total forces acting on each atom in the given list ? If yes, is it also
> eventually possible to obtain more detail list
> where is listed nonbond and bond part of the total force acting on each
> atom ?
You may want to check out the debug options. One in particular is the "dumpfrc" option, part of the &debugf namelist, which will print the total force on each atom, spitting it out to a file called "forcedump.dat".
As for how to get a breakdown of the forces by component, dumpfrc provides some of this information, though it's not comprehensive. It includes, I think, bond, angle and torsion forces. You could get other components of the force indirectly, for example by running the same calculation with and without the "zerochg" and "zerovdw" debugging options and calculating the difference.
HTH,
Ben
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Received on Tue Sep 14 2010 - 14:00:03 PDT
