[gmx-users] Reference group in COM pulling

[Erik Marklund]

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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