[gmx-users] force/time application for pull

[Justin Lemkul]

On 8/13/18 6:38 AM, Rakesh Mishra wrote:
> Hello Mark,
>
> Thank for  your clarification. Gromacs pulling has simple protocol for
> pulling
> using umbrella sampling. Where one can only get f/t and x/t . here t is
> linearly
> increases for both cases of force and distance. That actually not full fill
> the need of
> experimental pulling.

As Mark said, the feature you're asking for does not exist in GROMACS. 
It could probably be coded in rather easily if you wanted to do so yourself.

-Justin

>
> On Mon, Aug 13, 2018 at 3:26 PM Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
>> Hi,
>>
>> It's possible, but there is no code written for it.
>>
>> Mark
>>
>> On Mon, Aug 13, 2018, 12:47 Rakesh Mishra <rockinbhu at gmail.com> wrote:
>>
>>> Dear Justin.
>>>
>>> Thanks for your kind  advise.
>>> But why don't it is not  possible to apply the constant force which
>> should
>>> increases linearly (at each instant of time delta)
>>> like at
>>> t1 -f1
>>> t2-f2
>>> .
>>> .
>>> tn-fn
>>>
>>> and corresponding to that force we get extension for each increment of
>>> time in Gromacs. This is more relevant in order to map
>>> experimental work of unzipping or axial pulling of nucleic acid like
>>> DNA/RNA/protein.  Is it possible to build this protocol in Gromacs.
>>>
>>> On Thu, Aug 9, 2018 at 5:30 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>>>
>>>>
>>>> On 8/9/18 6:37 AM, Rakesh Mishra wrote:
>>>>> Dear all,
>>>>>
>>>>> Can anyone shed some light as ,Is it possible to apply force/time for
>>>>> pulling in gromacs. Means I want to pull my system in step wise . eg.
>>>>>     0 - t1     force applied f1
>>>>>     t1+dt  to t2     force f2
>>>>>     t2+dt  to t3     force f3
>>>>>     .
>>>>>     .
>>>>>     .
>>>>>     tn-1 +dt  to tn     force fn
>>>>>    Is it possible.
>>>> Not in a single run. You would have to run a simulation for interval 0
>> -
>>>> dt, generate a new .tpr file for the time period of (t1+dt) - t2, etc.
>>>>
>>>> -Justin
>>>>
>>>> --
>>>> ==================================================
>>>>
>>>> Justin A. Lemkul, Ph.D.
>>>> Assistant Professor
>>>> Virginia Tech Department of Biochemistry
>>>>
>>>> 303 Engel Hall
>>>> 340 West Campus Dr.
>>>> Blacksburg, VA 24061
>>>>
>>>> jalemkul at vt.edu | (540) 231-3129
>>>> http://www.thelemkullab.com
>>>>
>>>> ==================================================
>>>>
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>>>
>>> --
>>>
>>> *With Best-Rakesh Kumar Mishra*
>>> *  (RA)CSD  SINP Kolkata, India*
>>>
>>> *E-mail - rakesh.mishra at saha.ac.in <rakesh.mishra at saha.ac.in> *
>>>
>>> *Phone n. +91 9473662491, +918777496532*
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>

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

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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