[gmx-users] Gromacs on GPU

Justin A. Lemkul jalemkul at vt.edu
Sat Jan 28 21:05:01 CET 2012

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.


> 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.hall at ucl.ac.uk <mailto:benjamin.a.hall at ucl.ac.uk>


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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