[gmx-users] mdrun discrepancy

[Haberl Florian]

hi,


> After mdrun, I am expecting a .trr file. But the following happens:
>
> -------------------------------------------------------------------------------
> [guest at localhost Tub]$ mdrun -v -s pr -e pr -o pr -c after_em -g prlog >&
> pr.job&
> [1] 5477
> [guest at localhost Tub]$ ls
> #1JFF.gro#    #b4em.gro#  ener.edr     posre.itp    pr.mdp
> step-3.pdb
> 1JFF.gro      b4em.gro    md.log       #pr.edr#     #pr.tpr#
> 1JFF.pdb      emlog.log   #mdout.mdp#  pr.edr       pr.tpr
> #1JFF.top#    em.mdp      mdout.mdp    pr.job       #step-2.pdb#
> 1JFF.top      em.tpr      #out.gro#    #prlog.log#  step-2.pdb
> after_em.gro  em.trr      out.gro      prlog.log    #step-3.pdb#
> [guest at localhost Tub]$
> -------------------------------------------------------------------------------
>
> When I open the pr.job file, I read the following at the end:
>
> Wrote pdb files with previous and current coordinates
> Fatal error: Bond deviates more than half its own length
>
> Please point out the solutions.

your protein has to much energy, so it^s instable try to do more em or
more restraints in your pr simulation

>
> ps: Dear Mickael Krzeminski: You wrote "Moreover, if your protein does
> not move (I mean with ngmx), it is probably
> because you have only one frame in the trr file. That would mean that you
> save your trajectory only in the end of the trajectory. You have to swap
> the
> value in the mdp file." Please clarify. How do I swap a value?
>
> Dear Dr. Spoel: When I ran gmxcheck according to your suggestion, I get
> the following:
> ----------------------------------------------------------------------------
> Checking file em.trr
> trn version: GMX_trn_file
> Reading frame        time  101.000
> # Atoms  69395
> Last frame           time  101.000
>
>
> Item        #frames Timestep (ps)
> Step             1
> Time             1
> Lambda           1
> Coords           1
> Velocities       0
> Forces           1
> Box              1
>

You see here step = 1 so you only got 1 timestep, take a look at the
manuel you have to increase logging.



Greetings,

Florian

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 Florian Haberl              Universitaet Erlangen/Nuernberg
 Computer-Chemie-Centrum     Naegelsbachstr. 25, D-91052 Erlangen

 Mailto: florian.haberl AT chemie.uni-erlangen.de

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