calculating forces from dcd trajectory

From: BIN ZHANG (zhngbn_at_gmail.com)
Date: Wed May 20 2009 - 02:18:26 CDT

Dear All:

I'm doing some post-processing with the dcd trajectories, and one the
quantities I would like to get out of is the force, i.e., the force
felt by an alpha carbon.

One way I can imagine to obtain the force is using the option
*pairInteraction*, and choose the group1 to be a single alpha carbon.
However, this would only give me all the forces coming from the
nonbonded interactions.

The *loadtotalforces* command in the TclForceScript seems to be
another promising way. But one thing I'm not clear is whether tclforce
script requires to run real dynamics.

Perhaps I'm thinking this problem too hard. Is there any other way to
calculate the forces?

Any suggestion would be highly appreciated.

Thanks a lot.

Bin

  

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