[gmx-users] umbrella sampling tutorial

[Nima Soltani]

> On 3/11/15 4:17 AM, Ming Tang wrote:
> > Dear all,
> >
> > I was learning the Umbrella Sampling tutorial step by step on Gromacs 5.0.4.
> > Everything was fine until I got to the step five (run the continuous
pulling simulation).
> > Then I turned to the 5.0.4 manual, and tried to modify the pull code,
but failed.
> >
> > ; Pull code in tutorial
> > pull            = umbrella
> > pull_geometry   = distance      ; simple distance increase
> > pull_dim        = N N Y
> > pull_start      = yes           ; define initial COM distance > 0
> > pull_ngroups    = 1
> > pull_group0     = Chain_B
> > pull_group1     = Chain_A
> > pull_rate1      = 0.01          ; 0.01 nm per ps = 10 nm per ns
> > pull_k1         = 1000          ; kJ mol^-1 nm^-2
> >
> > ; COM pulling I modified
> > pull            = umbrella
> > pull_geometry        = distance  ; simple distance increase
> > pull_dim             = N N Y
> > pull_start           = yes       ; define initial COM distance > 0
> > pull_coord1-groups   = 2

Group 1 & 2  participating in reaction coordinate So it is wrong to state
just group 2 in pull_coord1-groups   = 2
change it to : pull_coord1_groups    = 1 2 

> > pull-group1-name     = Chain_B
> > pull_group2-name     = Chain_A
> > pull-coord1-rate     = 0.01      ; 0.01 nm per ps = 10 nm per ns
> > pull-coord1-k        = 1000      ; kJ mol^-1 nm^-2
> >
> > Fatal error:
> > Group Chain_B referenced in the .mdp file was not found in the index file.
> > Group names must match either [moleculetype] names or custom index group
> > names, in which case you must supply an index file to the '-n' option
> > of grompp.
> >
> > Could anybody tell me what's wrong with the COM pulling code I modified?
> >
Best Regards,
Nima Soltani
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Graduate Student of Physical Chemistry
Department of Chemistry,
Sharif University of Technology.
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