Steve Vivian wrote:
New to Gromacs.
Worked my way through the tutorial with relatively few issues until the
Equilibration stage. My system blows up!!
Returned to the Topology stage and rebuilt my system ensuring that I
followed the procedure correctly for the InflateGro process. It appears
to be correct, reasonable lipid area, no water inside my bilayer, vmd
shows a structure which appears normal (although I am new to this).
There are voids between bilayer and water molecules, but this is to be
expected, correct?
Energy Minimization repeatedly produces results within the expected range.
Again system blows up at equilibration, step 0 segmentation fault.
Regardless of whether I attempt the NVT or Anneal_Npt process (using the
provided mdp files, including the updates for restraints on the protein
and the lipid molecules).
I have attempted many variations of the nvt.mdp and anneal_npt.mdp files
hoping to resolve my issue, but with no success. I will post the log
information from the nvt.mdp file included in the tutorial.
Started mdrun on node 0 Tue Mar 8 15:42:35 2011
Step Time Lambda
0 0.00000 0.00000
Grid: 9 x 9 x 9 cells
Energies (kJ/mol)
G96Angle Proper Dih. Improper Dih.
LJ-14 Coulomb-14
8.52380e+01 6.88116e+01 2.23939e+01 -3.03546e+01
2.71260e+03
LJ (SR) Disper. corr. Coulomb (SR)
Coul. recip. Position Rest.
1.49883e+04 -1.42684e+03 -2.78329e+05 -1.58540e+05
2.57100e+00
Potential Kinetic En. Total Energy
Conserved En. Temperature
-4.20446e+05 *1.41436e+14 1.41436e+14 1.41436e+14
1.23343e+12*
Pres. DC (bar) Pressure (bar) Constr. rmsd
-1.56331e+02 5.05645e+12 1.18070e+01
As you can see the Potential Energy is reasonable, but the Kinetic
Energy and Temperature seem unrealistic.
I am hoping that this is enough information for a more experienced
Gromacs user to provide guidance.
Note: that I have tried all of the suggestions that I read on the
mailing list and in the "blowing up" section of the manual, specifically:
-reduced time steps in Equilibration Stages
-reduced Fmax during EM stage (down as low as 100kJ which did not help)
-modified neighbours list parameters
Any help is appreciated.
I can attach and forward any further information as required, please let
me know.
Which Gromacs version are you using? It looks like you're running in serial, is
that correct? Otherwise, please provide your mdrun command line. If you're
using version 4.5.3 in serial, I have identified a very problematic bug that
seems to affect a wide variety of systems that could be related:
http://redmine.gromacs.org/issues/715
I have seen even the most robust tutorial systems fail as well, as some new lab
members experienced the same problem. The workaround is to run in parallel.
-Justin
Regards,
Steve Vivian.
sviv...@uwo.ca
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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