[gmx-users] my big problem

[Tsjerk Wassenaar]

Hi Mark,

Apparently, my mind was strongly biased towards reports on "RMSD"
"radius of gyration" "sharp peaks", ignoring too much of what went
before "started to run". I fully agree that I was careless here. But
he seems to say he did a simulation of 20 ns and then wonders why the
RMSD plots are different. Hasn't heard of stochastic processes. In any
case, having a two-component system with sharp peaks in RMSD and RGYR
does indicate PBC jumps, though that doesn't justify my neglect of the
other matters.

Tsjerk


On 3/29/07, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> Hi Ozge, Mark,
>
> Mark is of course completely right regarding the MPI error.., you're
> messing up something. Where was my mind? Sharp peaks in the RMSD and
> radius of gyration plots may indicate jumps over the periodic
> boundaries. But, that should not be a cause for breaking a simulation.
> The only parameter you mentioned that could be linked to the stability
> of the simulation is the nstcomm, the others only control output.
>
> Of course you should try to understand what made your simulation
> crash, in stead of treating symptoms, possibly covering up some flaw
> in the set up of the simulation. Check the .log file.
>
> Tsjerk
>
> On 3/29/07, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> > ? wrote:
> > > Hi everybody,
> > >
> > > I have a problem with my molcule.I have protein- ligand complex.One of
> > > my friends works with the same ligand.First of all we use the same mdp
> > > files.We made the simulation.But my calculations were halted.This is the
> > > error :
> > > Error on node 1, will try to stop all the nodes
> > > Halting parallel program mdrun_mpi on CPU 1 out of 8
> > > 7 additional processes aborted (not shown)
> >
> > This is just a generic MPI error message. You haven't established what
> > has caused it yet. Try running the system for a short time on a single
> > processor, to eliminate parallelism as a source of the problems (you'll
> > need to re-grompp, of course).
> >
> > >  I only can think about the difference may be caused because of my
> > > protein -ligand complex is very big.It has 2 chains.
> > >
> > > After that I changed
> > > nstcomm ,nstxout ,nstvout ,nstfout, nstlog ,nstenergy,  nstxtcout    values
> > > than it started to run. But the graphics after the analyze
> > > part(rmsd,gyration...) are very bad.I saw very sharp and meaningless
> > > pics.
> >
> > Probably your topology is broken or your structure is insufficiently
> > minimized or equilibrated.
> >
> > >Then I would like to do the same thing with a paper.In this paper
> > > they made the calculation for 50 ps with position restarint.After they
> > > made for 50 ps without position restraint.At the end they made for 20 ns
> > > again full mdp.Idid the same.But the gyration and rmsd calculations are
> > > not the same.Again meaningless graphics.I have tried to solve the
> > > problems for two months.If anything exist to solve the problems I can
> > > send my mdp files.Is there a mistake for my mdp files?
> >
> > We can't tell yet, since you haven't told us any symptoms that are
> > useful diagnostically.
> >
> > Mark
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>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
>


-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623