[gmx-users] Clarification for the meaning of ncoords in GROMACS 5.0.4 pull code

[Sajeewa Pemasinghe]

Thank you very much. I really appreciate your help.

On Sun, Mar 26, 2017 at 6:16 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 3/24/17 1:54 PM, Sajeewa Pemasinghe wrote:
>
>> Hi,
>>
>> I have two molecules which are not moving in the z axis due to being
>> continuous across the periodic boxes. I want to keep the distance between
>> them fixed by pulling along x and y axes. So as I am pulling along x and y
>> axes does my ncoords = 2 ?  By going along with this logic as long as my
>> pull-geometry = distance, will the maximum number for ncoords be 3 (i.e.
>> pulling along all x, y , and z axes)? I really appreciate an explanation.
>>
>>
> The "pull-ncoords" option tells grompp how many biasing potentials there
> are, not anything to do with which Cartesian directions are biased.
>
> -Justin
>
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> Justin A. Lemkul, Ph.D.
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