[gmx-users] Distance restraint between two chains' com
renerwei at gmail.com
Thu Feb 5 12:51:42 CET 2015
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, 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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