[gmx-users] mdrun discrepancy

jaimin at iitb.ac.in jaimin at iitb.ac.in
Tue Feb 1 07:15:14 CET 2005

Dear all,

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 >&
[1] 5477
[guest at localhost Tub]$ ls
#1JFF.gro#    #b4em.gro#  ener.edr     posre.itp    pr.mdp       
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.

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
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       0 time  101.000
# Atoms  69395
Last frame          0 time  101.000

Item        #frames Timestep (ps)
Step             1
Time             1
Lambda           1
Coords           1
Velocities       0
Forces           1
Box              1
Thanking you,

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