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

[Li, Hualin]

problem solved.

Many 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: 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.

-Justin

> Best,
> 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 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
>
> --
> ========================================
>
> 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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