[gmx-users] force calculations in PMF

[deepak bapat]

Thank you Alex.

Deepak

On Wed, Jan 4, 2017 at 9:06 AM, Alex <nedomacho at gmail.com> 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 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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>>
>>
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-- 
Deepak U. Bapat