Re: calculating forces from dcd trajectory

From: Peter Freddolino (
Date: Thu May 21 2009 - 06:55:47 CDT

Hi Bin,
please disregard my previous email... I remember now why namdenergy only
allows you to use -nonb for two-selection runs... namd only prints the
nonbonded forces when using pair interactions, not all forces. So you'll
probably need to use tclforces with loadforces for what you're after.
You should try a couple simple test cases to make sure that it gives you
the results that you're after. Sorry for the confusion on my part.

BIN ZHANG wrote:
> Dear Peter:
> Thanks for your response.
> It seems to me that only the option *-nonb* available while there are
> two selections in namdEnergy plugin. In this case, would the sum of all
> the forces be outputed in the pairInteraction force column, or only the
> ones coming from nonbonded interactions?
> Thanks,
> Bin
> On May 20, 2009, at 4:51 AM, Peter Freddolino wrote:
>> 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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