[gmx-users] Center of mass: distance restrain for groups

[Justin A. Lemkul]

Li, Hualin wrote:
>  I am sorry about the last post, I mean "I am not sure about the word "pull                umbrella", is this command used in free energy calculation to do the sampling ?  I am not doing the free energy calculation, should I change something in the mdp file to modify it please?
> 

Using "pull = geometry" simply applies a harmonic potential between the two 
restrained species.  No free energy calculation is done unless you do a full 
free energy workflow and analyze using g_wham.

-Justin

> Thanks,
> Hualin
> ________________________________________
> From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Justin A. Lemkul [jalemkul at vt.edu]
> Sent: Monday, September 26, 2011 12:05 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Center of mass: distance restrain for groups
> 
> Li, Hualin wrote:
>> Dear GMX users,
>>
>>    How are you doing? I have a question about using distance restrain in GROMACS, have you ever use the distance restrain to between the protein and the center of mass of membrane. In gromacs, I can not find the option to choose the center of mass of specific groups like membrane.
>>     Any ideas please? Thank you very much for your help.
>>
> 
> Use the pull code.  Distance restraints cannot be applied between different
> molecules.
> 
> -Justin
> 
> --
> ========================================
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================