[gmx-users] pull code problem

[Berk Hess]

Hi,

Do you have another line with "pull =" somewhere in your mdp file?

PS You should switch to Gromacs 4.0.4, since it contains several small
bug fixes for the pull code.

Berk

> Date: Mon, 11 May 2009 12:38:35 +0300
> From: neamtuandrei at gmail.com
> To: gmx-users at gromacs.org
> Subject: [gmx-users] pull code problem
> 
> hello,
> 
> I am trying to do a pulling simulation with gromacs 4.0.2
> 
> I added the following lines to the  .mdp input file for grompp:
> 
> ...
> 
> pull                   =  constraint
> pull_geometry          =  distance
> pull_dim               =  Y Y Y
> pull_nstxout           =  10
> pull_nstfout           =  10
> pull_ngroups           =  2
> pull_group0            =  Protein
> 
> pull_group1            =  CA2+1
> pull_rate1             =  0.3
> 
> pull_group2            =  CA2+2
> pull_rate2             =  0.3
> 
> .....
> 
> when I run
> > grompp -f production_prm.mdp .......etc.
> 
> it does not recognize the keywords for pulling:
> 
> Ignoring obsolete mdp entry 'title'
> 
> Back Off! I just backed up neutr_RCK_Mthk_solv.04.mdout.mdp to
> ./#neutr_RCK_Mthk_solv.04.mdout.mdp.6#
> 
> WARNING 1 [file production_prm.mdp, line unknown]:
>   Unknown or double left-hand 'pull_geometry' in parameter file
> 
> WARNING 2 [file production_prm.mdp, line unknown]:
>   Unknown or double left-hand 'pull_dim' in parameter file
> 
> WARNING 3 [file production_prm.mdp, line unknown]:
>   Unknown or double left-hand 'pull_nstxout' in parameter file
> 
> WARNING 4 [file production_prm.mdp, line unknown]:
>   Unknown or double left-hand 'pull_nstfout' in parameter file
> 
> WARNING 5 [file production_prm.mdp, line unknown]:
>   Unknown or double left-hand 'pull_ngroups' in parameter file
> 
> WARNING 6 [file production_prm.mdp, line unknown]:
>   Unknown or double left-hand 'pull_group0' in parameter file
> 
> WARNING 7 [file production_prm.mdp, line unknown]:
>   Unknown or double left-hand 'pull_group1' in parameter file
> 
> WARNING 8 [file production_prm.mdp, line unknown]:
>   Unknown or double left-hand 'pull_rate1' in parameter file
> 
> WARNING 9 [file production_prm.mdp, line unknown]:
>   Unknown or double left-hand 'pull_group2' in parameter file
> 
> WARNING 10 [file production_prm.mdp, line unknown]:
>   Unknown or double left-hand 'pull_rate2' in parameter file
> 
> .......
> 
> It appears that grompp doesnot recognize any of these keywords...
> 
> Does anybody can help?
> 
> Thank you
> Andrei
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