[gmx-users] my big problem

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Mar 29 10:02:51 CEST 2007

Hi özge,

Thank you for being more specific on the error than last time.
Apparently, from what you say now, it is evident that you're dealing
with the "my protein jumps out of the solvent" error reported (many
times) earlier on this list. Look for threads like that on the gromacs
user list, read about periodic boundary conditions and have a look at
trjconv (notably the option -pbc nojump).

Reading a bit more about the background of things will also help you
phrase your questions more clearly, as well as it will help you find
answers yourself.



On 3/29/07, özge kül <ozgekul8233 at yahoo.com> 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)
>  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.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?
> thank you ..
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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

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