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

[WT Ren]

Dear Justin:

Sorry to bother you again

When I did a long flat-bottom distance restraint(about 2nm),
I got the error message: “There is no domain decomposition for 8 nodes....”

So is there any way to do a long distance restraint properly.

     Best regards

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 7:51 PM, WT Ren <renerwei at gmail.com> wrote:

> 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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>