[gmx-users] Distance restraint between two chains' com
renerwei at gmail.com
Fri Feb 6 14:47:36 CET 2015
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.
Weitong* Ren, PhD student*
Laboratory of Biophysics
Department of Physics
Nanjing, Jiangsu, PR China
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
> So it seems that I have to choose some atoms from the two chains
> and do distance restraint on these atoms.
> Weitong* Ren, PhD student*
> Laboratory of Biophysics
> Department of Physics
> *Nanjing University*
> Nanjing, Jiangsu, PR China
> 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
>>> harmonic potential, while the distance restraint seems can not be
>>> 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:
>> 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
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