[gmx-users] pulling in opposite direction

[Justin Lemkul]

On 10/5/18 12:47 AM, Rakesh Mishra wrote:
> Dear Justin thanks for ur reply.
> Which means in this case,both group will act as a reference group for each
> other.
>
> Then now my question is, why without using two biasing potential, in case
> of using one
> biasing potential for two group, If I do not constrained reference group
> then it automatically
> move in the opposite direction w.r.t pulling group.

I feel like I've already explained how all of this works. The bias is 
applied to the specified groups, and they evolve however they're going 
to under the influence of the applied force.

It may help to stop thinking concretely in terms of a "reference" and a 
"pulled" group. That's a conceptual convention that is actually somewhat 
outdated now that GROMACS supports multiple, simultaneous biasing 
potentials. Each group defines the end of a reaction coordinate. Their 
relative positions matter in terms of defining the direction of the 
bias, hence the "reference" and "pulled" nomenclature. But again, I 
think that by enforcing such nomenclature, it's a bit misleading.

-Justin

>
> On Thu, Oct 4, 2018 at 6:48 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> On 10/4/18 3:09 AM, Rakesh Mishra wrote:
>>> Dear all.
>>>
>>> How it is possible to pull reference group as well as pull group using
>>> gromacs protocol simultaneously in opposite direction using umbrella
>>> protocol
>>> of pulling. So far non of the Gromacs expertise  have given the answer of
>>> this question. Hoping from response
>>>
>> If you want to pull two things in opposite directions, you need two
>> biasing potentials.
>>
>> -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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>

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

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

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