On 1/08/2012 5:49 PM, rama david wrote:
Is it possible to install Gromacs in parrallel mode in following system
in order to perform Replica Exchange Molecular Dynamics ( REMD )???...
1. Intel I5 processor, Dell Desktop.
and
2. Dell precision T 3500 Intel (R)Xeon (R)W3670 3.2 GHZ,
Thank you Mark for your Reply..
I install open-mpi through Ubuntu software package ..
I know that these are not officially supported by the GROMACS team...
I made two different tpr file with the grompp command that has two
different temp..
( 300 K and 310 K) ..topol0.tpr topol1.tpr as your
On 1/08/2012 7:41 PM, rama david wrote:
Thank you Mark for your Reply..
I install open-mpi through Ubuntu software package ..
I know that these are not officially supported by the GROMACS team...
I made two different tpr file with the grompp command that has two
different temp..
( 300 K and
Thank you Mark for reply..
I run mdrun and mpirun with following command. I pasted output also..
Please help me to parse it..
1. mdrun -v -deffnm topol1
2. mpirun -np 4 mdrun -v -deffnm topol1
1.mdrun -v -deffnm topol1
step 30, will finish Wed Aug 1 16:49:28 2012
Average load
Both are probably using 4 cores, the first one as threads, the second via mpi.
However, in the second one you are using 16 threads to run 4 copies of
the same simulation, 4 threads each, thus getting performance similar
(or less) to using only one core. When using mpi, you should use
mdrun_mpi
On 1/08/2012 8:36 PM, rama david wrote:
Thank you Mark for reply..
I run mdrun and mpirun with following command. I pasted output also..
Please help me to parse it..
1. mdrun -v -deffnm topol1
2. mpirun -np 4 mdrun -v -deffnm topol1
1.mdrun -v -deffnm topol1
step 30, will
Thank you for reply and your suggestion..
As I mentioned earlier I installed Gromacs-openmpi 4.5.5 from Ubuntu
software package manager
So I want to just check is it performing REMD or not???
So as per previous suggestion of Mark ...
I made two tpr file that has two different temp 300 k and
On 2/08/2012 1:02 AM, rama david wrote:
Thank you for reply and your suggestion..
As I mentioned earlier I installed Gromacs-openmpi 4.5.5 from Ubuntu
software package manager
So I want to just check is it performing REMD or not???
So as per previous suggestion of Mark ...
I made two tpr
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