Re: calculating forces from dcd trajectory

From: BIN ZHANG (zhngbn_at_gmail.com)
Date: Wed May 20 2009 - 12:18:20 CDT

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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