[gmx-users] force calculations in PMF

[deepak bapat]

Dear gmx users

If I use

pull = constraint

then am i correct in assuming that the bias potential will not be used. So
the WHAM method can not be used.

If I do not have the bias potential then can I find PMF by doing the
constraint force integration.

How can I find the constraint force from pull code?

Regards

Deepak





On Wed, Jan 4, 2017 at 7:36 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
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-- 
Deepak U. Bapat