Re: calculating forces from dcd trajectory

From: BIN ZHANG (zhngbn_at_gmail.com)
Date: Thu May 21 2009 - 12:40:15 CDT

Hi, Peter :

Thanks for your comment. ;-)

Bin

On May 21, 2009, at 4:55 AM, Peter Freddolino wrote:

> 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.
> Best,
> Peter
>
> 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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