[gmx-users] REMD error

[bharat gupta]

Thanks for the advice I re-complied everything again with static libraries
and the installation went fine. But while executing the following command I
am again getting error :-


mdrun_mpi mdrun  -s prefix_.tpr -multi 20 -replex 500 -v


Fatal error:
The number of nodes (1) is not a multiple of the number of simulations (3)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

"BioBeat is Not Available In Regular Shops" (P.J. Meulenhoff)

Halting program mdrun_mpi

gcq#155: "BioBeat is Not Available In Regular Shops" (P.J. Meulenhoff)

application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0


I am trying to simulate 5 replicas and I have 4 cpu .



On Thu, Jan 12, 2012 at 1:37 PM, lina <lina.lastname at gmail.com> wrote:

> On Thursday 12,January,2012 08:54 AM, bharat gupta wrote:
>
>> Hi,
>>
>> I am trying to run a REMD of a peptide. But while executing the
>> following command after nvt and npt equilibration , I am getting the
>> following error:-
>>
>> mdrun_mpi mdrun -s prefix_.tpr -multi 20 -replex 1000
>> mdrun_mpi: error while loading shared libraries: libgmx_mpi.so.6: cannot
>> enable executable stack as shared object requires: Permission denied
>>
>
> Can you run a normal md smoothly?
> try:
> mdrun_mpi mdrun -deffnm prefix_0
>
> if it works, then some of your trajectories not sound. means system does
> not equilibrium well.
>
>
>>
>> Can anybody suggest me how could I rectify this error.
>>
>> --
>> Bharat
>>
>>
> --
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-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46010 at yahoo.com
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