[gmx-users] different versions- different output!

jojo J joojoojooon at gmail.com
Thu Jan 20 14:33:02 CET 2011

Hello all,

I am a little confused since I am not getting the same output from the same
input files using two different versions (the most recent one: 4.5.3 and
4.0.7). I am using two different machines and size of data generated from
these simulations are not the same either. Below is the output of grommp on
4.5.3 which results in segmentaion fault error. The other version gives no
error and I get trr file without any problem. System is stable and it is
equilibrated.. Can you please help me and guide me how to deal with the
following errors and why is this happening?

many many thanks,

NOTE 1 [file md-.mdp]:
  nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
  nstcomm to nstcalcenergy

Generated 332520 of the 332520 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 332520 of the 332520 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Polymer'
Velocities were taken from a Maxwell distribution at 300 K
Number of degrees of freedom in T-Coupling group System is 8685.00

NOTE 2 [file md.mdp]:
  The sum of the two largest charge group radii (0.204120) is larger than
  rlist (1.100000) - rvdw (1.000000)

This run will generate roughly 35 Mb of data
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