[gmx-users] force calculations in PMF

[Justin Lemkul]

On 1/3/17 10:36 PM, Alex wrote:
> Since I don't use WHAM or even know what it is, I can only guess that feeding
> pullf data sets the COM force as a function of time. Conversely, GMX reports COM
> pullf data when pulling is set up via pull code. And that is the pulling force
> acting upon the COM of the _pulled object_. So, I can guess here that you're
> supplying the force data for the COM of _the group subject to pulling_. It makes

More precisely, it is the force acting on the spring connecting the two groups.

-Justin

> very little sense to me that a force would be prescribed for the entire system
> when the objective is to artificially move one subsystem relative to another.
>
> This assumes I understood your question. :)
>
> Alex
>
>
> On 1/3/2017 8:22 PM, deepak bapat wrote:
>> HI Alex!
>>
>>
>>
>> OK.. :-)
>>
>> Let me try to put it this way.
>>
>> In WHAM method we supply pullf files.
>>
>> I had doubt regarding forces listed in those files.
>>
>> Whether these values are for the entire system or the forces acting on the
>> particular group which is being pulled away.
>>
>> Regards
>>
>> Deepak
>>
>>
>>
>>
>>
>>
>> On Wed, Jan 4, 2017 at 8:46 AM, Alex <nedomacho at gmail.com> wrote:
>>
>>> There's a reason no one is replying: we can't understand your question. :)
>>>
>>>
>>>
>>> On 1/3/2017 8:09 PM, deepak bapat wrote:
>>>
>>>> Dear Gromacs users
>>>>
>>>> I had a doubt regarding pull code.
>>>>
>>>> Which force values are considered while calculations? ensemble average
>>>> values of the entire system or the forces acting on the group/atoms under
>>>> consideration.
>>>>
>>>> Regards
>>>>
>>>> Deepak
>>>>
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>>
>>
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================