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

Li, Hualin Hualin.Li at uth.tmc.edu
Tue Sep 27 20:23:35 CEST 2011

Hi, Justin,

     Thank you very much for your reply. I use the following pull code in my mdp file:
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_DUPC_CHOL ;# the reference group - the membrane
pull_weights0    =   0 ;# use mass as weight
pull_pbcatom0    =   -1 ;# or -1 - important for PBC of groups larger than half box,
                      ;# as here for membrane (see manual)
pull_group1      =   H4 ;# 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 ,  when I use grompp to pre-compile it , the error "Fatal error:
Number of weights (1) for pull group 0 'DPPC_DUPC_CHOL' does not match the number of atoms (86016)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors"  comes out.

      I change pull_weights0 to pull_weights0=86016, but it still doesn't work. Could you please tell me the reason.
      Thank you very much.



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 1:32 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Center of mass: distance restrain for groups

Justin A. Lemkul wrote:
> 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

Sorry, that should read "pull = umbrella" :)



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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