[gmx-users] Problem with OpenMP+MPI

[jesmin jahan]

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).

Thanks,
Jesmin

On Wed, Feb 27, 2013 at 2:59 AM, Carsten Kutzner <ckutzne at gwdg.de> wrote:
> Hi,
>
> 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 ";")
>
> Carsten
>
>> 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!
>>
>> Thanks,
>> Jesmin
>> --
>> Jesmin Jahan Tithi
>> PhD Student, CS
>> Stony Brook University, NY-11790.
>> --
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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
> http://www.mpibpc.mpg.de/grubmueller/kutzner
> http://www.mpibpc.mpg.de/grubmueller/sppexa
>
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-- 
Jesmin Jahan Tithi
PhD Student, CS
Stony Brook University, NY-11790.