Re: calculating forces from dcd trajectory

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed May 20 2009 - 06:51:11 CDT

Hi Bin,

BIN ZHANG wrote:
> 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.
Why? If group1 is the CA atom and group2 is everything else in the
system, you should get what you want.
>
> 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.
>
I believe this should work as well, but you might want to verify it with
a simple test case (and pairInteractions should give a simpler way to
get the same thing).

Best,
Peter

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