[gmx-users] Problem with OpenMP+MPI
shraban03 at gmail.com
Wed Feb 27 14:53:43 CET 2013
Thanks Crasten for your reply.
Even after removing comment, I am getting the same error message.
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).
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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Jesmin Jahan Tithi
PhD Student, CS
Stony Brook University, NY-11790.
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