[gmx-users] Reference group in COM pulling

[WT Ren]

Erik；
     Thanks very much！

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 Tue, Nov 25, 2014 at 9:18 PM, Erik Marklund <erik.marklund at chem.ox.ac.uk>
wrote:

> No. The protein is probably not fixed in experiments.
>
> Erik
>
> On 25 Nov 2014, at 12:55, WT Ren <renerwei at gmail.com> wrote:
>
> > Justin：
> > Thanks for your reply,
> > so if I want to compare the results from simulation to experiment‘s，
> should
> > I fixed the reference group?
> > moreover， if I fixed the reference group，do I need to remove the
> > restriction on the center of mass motion?
> >
> > 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 Tue, Nov 25, 2014 at 8:31 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> >>
> >>
> >> On 11/25/14 3:33 AM, WT Ren wrote:
> >>
> >>> Dear all:
> >>>       Recently,  I'm using COM pulling to unfold a protein. So I'm
> >>> wondering how the gromacs deal with the reference group. Is the
> reference
> >>> group fixed, constrained or free?
> >>>
> >>
> >> Free, unless you do something to fix or restrain it.
> >>
> >> -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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