On 3/7/13 1:17 PM, Miguel Ángel Mompeán García wrote:
2013/3/4 Justin Lemkul <jalem...@vt.edu>
Dear Justin,
With 4.5.5 the jobs have completed. I am going to repeat them with 4.6.1
If you find something weird in the mdp file or require further explanations
on the points do mention I will do my best to provide the necessary info.
Right below are the comments:
In that case, it's probably something worth pursuing. Having the new
version fail when an older version works is curious. Can you please
provide all of the following details:
1. Compilers used to build Gromacs
2. Hardware description
These lines are from the CMakeOutput.log file:
The system is: Linux - 2.6.32-5-amd64 - x86_64 (*****)
Compiling the C compiler identification source file "CMakeCCompilerId.c"
succeeded.
Compiler: /usr/bin/gcc
cc -v: gcc version 4.4.5
3. mdrun command
4. Complete .mdp file
grompp -f minimize.mdp -c Mut3.gro -o em.tpr -p topol.top
mdrun -v -deffnm em
The minimize.mdp file:
integrator = steep
emtol = 1000.0
emstep = 0.01
nsteps = 50000
nstlist = 1
ns_type = grid
rlist = 1.0
coulombtype = PME
rcoulomb = 1.0
rvdw = 1.0
pbc = xyz
Does the .tpr file run on a machine with different hardware or compilers? The
GCC version is outdated, though in principle should work fine. If the failure
consistently happens on your machine (and especially if it happens on other
machines), please file a bug report on redmine.gromacs.org and include a .tpr
file and all of the information posted above.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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