[gmx-users] Center of mass: distance restrain for groups
Hualin.Li at uth.tmc.edu
Tue Sep 27 22:41:40 CEST 2011
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Justin A. Lemkul [jalemkul at vt.edu]
Sent: Tuesday, September 27, 2011 2:46 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Center of mass: distance restrain for groups
Li, Hualin wrote:
> 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.
If you're not doing any special weighting, omit this keyword.
> 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
>> 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
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> gmx-users mailing list gmx-users at gromacs.org
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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