[gmx-users] pull code problem

[Berk Hess]

Hi,

Maybe there is an older grompp in your path.
Type grompp -h to see which version you are using.
And:
which grompp
to see where it comes from.

Berk

> Date: Mon, 11 May 2009 13:03:07 +0300
> From: neamtuandrei at gmail.com
> To: gmx-users at gromacs.org
> Subject: [gmx-users] pull code problem
> 
> Hi Berk,
> thank you for the reply
> 
> here is my mdp file:
> 
> ;
> 
> ;	User aneamtu	
> 
> ;	Joi, 7 mai - 2009
> 
> ;	Input file
> 
> ;
> 
> title                  =  Production_runs
> 
> ;define                 =  -DPOSRES -DPOSRES_CA2+_IONS
> 
> 
> 
> ;constraints           =  all-bonds
> 
> 
> 
> integrator             =  md
> 
> dt                     =  0.001	
> 
> nsteps                 =  50000	
> 
> 
> 
> nstcomm                =  1
> 
> nstxout                =  1000
> 
> nstvout                =  1000
> 
> nstfout                =  1000
> 
> nstlog                 =  500
> nstxtcout              =  50
> xtc_grps               =  Protein_ions
> 
> 
> nstenergy              =  100
> 
> nstlist                =  10
> 
> ns_type                =  grid
> 
> 
> coulombtype            =  PME
> 
> rlist                  =  1.0
> 
> rcoulomb               =  1.0
> 
> rvdw                   =  1.0
> optimize_fft           =  yes
> 
> 
> Tcoupl                 =  v-rescale
> 
> tc-grps		       =  Protein   SOL   ions
> 
> tau_t                  =  0.1       0.1   0.1
> 
> ref_t                  =  310       310   310
> 
> 
> 
> energygrps             =  Protein  SOL CA2+ NA+ CL-
> 
> 
> 
> Pcoupl                 =  berendsen
> 
> Pcoupltype             =  isotropic
> 
> tau_p                  =  0.5
> 
> compressibility        =  4.5e-5
> 
> ref_p                  =  1.0
> 
> 
> 
> gen_vel                =  no
> 
> gen_temp               =  310.0
> 
> gen_seed               =  173529
> 
> 
> 
> 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
> 
> 
> I do not understand what I do wrong..
> Should I use a -pi pull.ppa file like in gromacs 3.x ?
> 
> Andrei
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