[gmx-users] Problem with OpenMP+MPI
jalemkul at vt.edu
Wed Feb 27 14:55:41 CET 2013
On 2/27/13 8:53 AM, jesmin jahan wrote:
> Thanks Crasten for your reply.
> Even after removing comment, I am getting the same error message.
You need to re-create the .tpr file after modifying the .mdp file. If you're
getting the same error, you're using the wrong .tpr file.
> Do you have any sample .mdp file that can be used while using MPI+OPENMP?
> I am trying to compute the GB energy (implicit solvent based).
Note that implicit solvent calculations can be run on no more than 2 processors.
You'll get a fatal error if you try to use more.
> On Wed, Feb 27, 2013 at 2:59 AM, Carsten Kutzner <ckutzne at gwdg.de> wrote:
>> On Feb 27, 2013, at 6:55 AM, jesmin jahan <shraban03 at gmail.com> wrote:
>>> Dear Gromacs Users,
>>> I am trying to run the following command on gromacs 4.6
>>> mdrun -ntmpi 2 -ntomp 6 -s imd.tpr
>>> But I am getting the following error
>>> OpenMP threads have been requested with cut-off scheme Group, but
>>> these are only supported with cut-off scheme Verlet
>>> Does any one know a solution to the problem?
>>> I am using the following .mdp file
>>> constraints = none
>>> integrator = md
>>> ;cutoff-scheme = Verlet
>> yes, as the note says, use the verlet cutoff scheme (by deleting the ";")
>>> pbc = no
>>> dt = 0.001
>>> nsteps = 0
>>> rcoulomb = 300
>>> rvdw = 300
>>> rlist = 300
>>> nstgbradii = 300
>>> rgbradii = 300
>>> implicit_solvent = GBSA
>>> gb_algorithm = HCT ;
>>> sa_algorithm = None
>>> gb_dielectric_offset = 0.02
>>> ;optimize_fft = yes
>>> energygrps = protein
>>> Please let me know what to change so that it runs perfectly!
>>> Jesmin Jahan Tithi
>>> PhD Student, CS
>>> Stony Brook University, NY-11790.
>>> gmx-users mailing list gmx-users at gromacs.org
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>> Dr. Carsten Kutzner
>> Max Planck Institute for Biophysical Chemistry
>> Theoretical and Computational Biophysics
>> Am Fassberg 11, 37077 Goettingen, Germany
>> Tel. +49-551-2012313, Fax: +49-551-2012302
>> gmx-users mailing list gmx-users at gromacs.org
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Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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