[gmx-users] Pull Code Error "unknown left hand"

[Mark Abraham]

Hi,

Things change between versions when we recognize limitations of old
decisions. 5.0 certainly recognizes pull-ngroups, so I think you were using
a non-matching grompp at some point. You do have the option of reading the
.mdp documentation for the version you're using. :-) (Of course, if it's
out of date, let us know and we'll fix it!)

Mark

On Mon, Oct 5, 2015 at 9:10 AM Kutzner, Carsten <ckutzne at gwdg.de> wrote:

> Hi,
>
> take a look at the mdout.mdp grompp output file. There you should see
> how the pull-related parameters are called in the version you were using.
> Maybe you just need to use minus signs instead of the underlines.
>
> Best,
>   Carsten
>
>
> > On 05 Oct 2015, at 04:25, Stella Nickerson <stella.nickerson at gmail.com>
> wrote:
> >
> > I am attempting to pull a particle across a simulation box. I did it
> > several times with version 4.6.3 but this is my first attempting to do it
> > with version 5.0.4.
> >
> > I modified my mdp file for the new version based on the updated tutorial
> (
> >
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html
> ).
> > My pull code looks like this:
> >
> > ; Pull code
> > pull                    = yes
> > pull_ngroups            = 2
> > pull_ncoords            = 1
> > pull_group1_name        = DMY
> > pull_group2_name        = DNP
> > pull_coord1_type        = umbrella
> > pull_coord1_geometry    = direction_periodic
> > pull_coord1_groups = 1 2
> > pull_coord1_dim         = N N Y
> > pull_coord1_rate        = 0.01
> > pull_coord1_k           = 1000
> > pull_start              = yes
> >
> > I am getting an error message and several warnings. The error reads
> > "Invalid enum 'yes' for variable pull, using 'no' Next time use one of:
> > 'no' 'umbrella'  'constraint 'constant force.'
> >
> > The warnings read "unknown left-hand 'pull_ngroups' in parameter file",
> > with similar warnings for the other left-hand terms.
> >
> > I tried to compile a version using my old pull code from the earlier
> > version just to see what would happen and it gave fewer warnings, though
> it
> > didn't recognize "pull_vec1." So neither the old options nor the new
> > options work.
> >
> > I would love some clarification on this issue.
> >
> > Thanks,
> >
> > Stella Nickerson
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