[gmx-users] Distance restraint between two chains' com

[WT Ren]

Dear Justin:

Many thanks for your reply.
I would like to test the new feature, but I have no much spare time
recently.
So it seems that I have to choose some atoms from the two chains
seperately,
and do distance restraint on these atoms.

Weitong* Ren, PhD student*
Laboratory of Biophysics
Department of Physics
*Nanjing University*
Nanjing, Jiangsu, PR China
210093
tel : +86 025 8359 7226
*wtren at biophy.nju.edu.cn <wtren at biophy.nju.edu.cn>*

On Thu, Feb 5, 2015 at 7:10 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 2/5/15 2:39 AM, WT Ren wrote:
>
>> Dear Gromacs Users,
>>
>> I am trying to apply a distance restraint between two chains' center of
>> mass to  prevent them diffusing far away from each other. As I known, the
>> pull code seems only can restrain the distance to a reference distance
>> with
>>   harmonic potential, while the distance restraint seems can not be
>> applied
>> to center of mass.
>>
>> So can anyone help on this issue?
>>
>>
> I am assuming that you want to apply some sort of flat-bottom potential,
> to be applied only when the chains move a certain distance.  Indeed the
> pull code cannot do that at present, but a flat-bottom potential is in
> development if you want to test it:
>
> https://gerrit.gromacs.org/#/c/3947/
>
> -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
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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