Re: [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  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
>
> --
> ==
>
> 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
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
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Re: [gmx-users] Clarification for the meaning of ncoords in GROMACS 5.0.4 pull code

[Justin Lemkul]

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

--
==

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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

[Sajeewa Pemasinghe]

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.

Thank you very much

Sajeewa Dewage
New York University - Abu Dhabi
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