[gmx-users] Unreadable trajetory

Jernej Zidar jernej.zidar at gmail.com
Wed Mar 14 07:59:24 CET 2012

  I'm testing a forcefield with a combination of CPT and NVT MD
simulations of a polymer in water. I adopted the equilibration steps
form the CHARMM equilibration steps:
1. Fix solute (using "define  = -DPOSRES" ).
a) 10.000 steps of steepest descent minimization
b) 10.000 steps of conjugated gradient minimization with a steepest
descents every 1000 steps
c) 100.000 steps of NVT MD during which I slowly heat the system to 300 K
d) 100.000 steps of CPT MD
e) 100.000 steps of NVT MD
f) 100.000 steps of CPT MD
g) 100.000 steps of NVT MD
h) 100.000 steps of CPT MD

2. Remove contraints and repeat steps a-h.

  The problem I'm having is that I cannot visualize the trajectories
from step 2.e) onwards with VMD simply segfaulting. While it may well
be a VMD issue but I can't visualize the trajectory using ngmx (blank
screen) either, so it's an issue either with my inputs or Gromacs.

  I tried to use trjconv tool to adjust the centering or remove the
PBC or save just the polymer residues but the utility always fails
with: WARNING no output, last frame read at t=200.
  Checking the run log file did not reveal any errors. Checking the
EDR file revealed no jumps in any of the enery terms.

  What's most surprising, is that I can visualize the GRO file that is
generated at the end of the simulation.

  The relevant files are on the following links:
- MDP: http://dl.dropbox.com/u/5761806/md-nvt-2-nofix.mdp
- LOG: http://dl.dropbox.com/u/5761806/wpoly-2x-box-ions-nvt-nofix-2.log
- TPR: http://dl.dropbox.com/u/5761806/wpoly-2x-box-ions-nvt-nofix-2.tpr

   I use GROMACS 4.5.5, the system is electrically neutral. To prepare
a new TPR file a use the GRO file from the previous run.

Thanks in advance for any tip,
Jernej Zidar

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