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

Li, Hualin Hualin.Li at uth.tmc.edu
Mon Sep 26 20:08:03 CEST 2011

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?


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



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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