So I have tried different methods for improving minimization - vacuum or gb
but it seems like the minimization gets stuck in a local minimum with a
rather high Gmax around 10. When I look at the tutorial, the Gmax value is
also rather high ~ 14 so I do not know quite what to expected?
In order to equilibrate the system I am a md simulation with T=10K in
implicit solvent in order to get out of any local minima where I have been
stuck - so here I would monitor the total energy which should converge what
other parameters should be monitored or put in another way which parameters
should absolutely not be positive? The vdw is negative as well as eelec
well.
On Fri, Jul 30, 2010 at 6:52 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> What is the type of the hydrogen? What vdw params does that
> type have? It's unlikely that it is trying to merge with another
> hydrogen, so if there's a way to print out crds for each step
> of min, it would be interesting to watch the movie in VMD and see
> what is happening. Failing that, you could set the maxcyc to
> one step less than you see blowup, so that you'd have a restrt
> from right before the blowup to look at (i.e. make pdb). The
> movie will be more instructive.
>
> It might be interesting to run a few hundred steps of 10K MD
> to see if it loosens things up.
>
> Bill
>
> > So I get some very high Gmax value during minimization for a hydrogen
> > atom(HG2) bound to a Arginine - when I look at the pdb file the distance
> > between its nearest neighbor is 1.76 Å to a hydrogen on proline residue
>
> > I use constraints for the hydrogen bond length through shake
> > SHAKE:
> > ntc = 2, jfastw = 0
> > tol = 0.00001
>
> > the rms gradient is 5.8 which is pretty high. The vdwaals are negative
> > -7764. I have not yet added any extra water molecules only the crystal
> ones
> > not having too high clashing. Are there any debugging in order to
> identify
> > the clash - is it vdw or something else and how to resolve that?
>
> > On Tue, Jul 27, 2010 at 8:53 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
> > > > Furthermore, the residues around are displaced which
> > > > they are not supposed to do - I have included low vdw radii and the
> > > bonding
> > > > energy has a very high force constant (100 ) - can I get the clashing
> > > part
> > > > of Gmax out?
> > >
> > > The atom indicated by GMAX is the one to focus on.
> > > What is it? What type? What vdw params? What bonded to?
> > > Are you expecting that a high bonding force constant will somehow
> > > compensate for low vdw radii? That would only work in a highly
> > > constrained system, likely with just a few atoms that could not
> > > form vdw contacts.
> > >
> > > > When I look in the pdb it seems fine so there is a clash I am
> > > > not able to see.
> > >
> > > The clash probably develops as atoms are pulled together.
> > > If you print crds for every step of md or min, you likely will
> > > see the problem developing.
> > >
> > > Bill
> > >
>
>
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Received on Mon Aug 02 2010 - 01:30:03 PDT
