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

[Li, Hualin]

Hi, Justin,

     Thank you very much for your reply. I want to use the the pull code like this to do the restrain:


"pull                umbrella
pull_geometry       distance
pull_dim            Y Y Y ;# 3D
pull_start          yes ;# add COM distance to initial value (initial value = equilibrium value)
pull_ngroups        1 ;# excluding the reference
pull_group0         DPPC ;# the reference group - the membrane
pull_weights0       0 ;# use mass as weight
pull_pbcatom0       0 ;# or -1 - important for PBC of groups larger than half box,
                      ;# as here for membrane (see manual)
pull_group1         Protein ;# the protein
pull_weights1       0 ;# use mass as weight
pull_pbcatom1       0 ;# here is no issue since protein is smaller than half the box
pull_rate1          0 ;# do not pull, just maintain distance!
pull_k1             50 ;# kJ mol^(-1) nm^(-2)"

However, I am 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?

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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