Dear Ben,
thanks a lot for your valuable info !
Best,
Marek
Dne Tue, 14 Sep 2010 22:45:39 +0200 Ben Roberts <roberts.qtp.ufl.edu>
napsal/-a:
> 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 - 14:30:04 PDT
