[gmx-users] Incorrectly added water molecule by genbox.

[Mark Abraham]

The standard advice is here
http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation.
You should work out what the common theme is and address that, rather than
make random changes. You ought to have no need of frozen groups during EM -
you are trying to relax your starting configuration!

Mark


On Thu, Jul 3, 2014 at 12:39 PM, Dawid das <addiw7 at googlemail.com> wrote:

> Thank you Mark but it seems that removing one water molecule does not do
> any good. I removed another one and the error arises again for another one.
> What else can I do if water does not settle during minimization?
> That's my minimize.mdp file.
>
> title                    = minimization of mCherry
> ; this is a comment
> integrator               = cg ; (other: steep, l-bfgs)
> emtol                    = 1000
> emstep                   = 0.01
> nsteps                   = 2000
> nstlist                  = 1
> ns_type                  = grid
> nstenergy                = 50
> rlist                    = 1.0
> coulombtype              = PME
> rcoulomb                 = 1.0
> rvdw                     = 1.0
> pbc                      = xyz
> freezegrps               = Protein
> freezedim                = Y Y Y
>
>
>
> 2014-07-03 9:55 GMT+02:00 Mark Abraham <mark.j.abraham at gmail.com>:
>
> > On Thu, Jul 3, 2014 at 9:17 AM, Dawid das <addiw7 at googlemail.com> wrote:
> >
> > > Hi,
> > >
> > > I have a following issue. Genbox seems to add a water molecule inside
> > small
> > > protein cavity and it does not belong there. Can I manually remove it
> > from
> > > *gro file?
> >
> >
> > Yes, but you need to make a matching change to the [molecules] section of
> > any matching .top file.
> >
> >
> > > What with the numbering of residues in this situation?
> >
> >
> > Immaterial. The only important thing in such cases is that there is a
> > change; the values or the delta-value is not noticed.
> >
> > Mark
> >
> >
> > > The
> > > problem is that this water molecule can't be settled during
> minimization
> > > and it spoils everything.
> > >
> > > Dawid
> > > --
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