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-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Justin A. Lemkul [jalem...@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
========================================
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