Benjamin Hall wrote:
Justin A. Lemkul wrote:
We get junk output with 4.5.4 if the box size is set to zero, for some
odd
reason, though in principle it should be ignored with "pbc = no" in
the .mdp
file. Using any non-zero box results in usable results. Our OpenMM
version is
the same, but Cuda is in the 3.x series (can't remember off the top of
my head,
sorry).
I've tried setting the box size in the gro file but that doesn't seem to
work (100x100x100nm). Which compiler did you use? I realise that this is
an unlikely source of trouble but it's another variable to eliminate in
testing.
Ours is gcc-4.4.6 on a local machine using Cuda 3.2. On our university's GPU
cluster, the installation was done with gcc-4.3.4 and Cuda 3.1. I have not
tested Cuda 4.0, though it has recently become available to us so it might be
worth a shot to see if this is another issue.
-Justin
I'll update issue 568 on redmine, which has been closed but appears to
be this problem.
Thanks & best wishes
Ben
--
Dr Benjamin A Hall
Centre for Computational Science, Department of Chemistry, UCL
benjamin.a.h...@ucl.ac.uk <mailto:benjamin.a.h...@ucl.ac.uk>
--
========================================
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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