Re: [gmx-users] About system requirement to gromacs

2012-08-01 Thread Mark Abraham
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,

Re: [gmx-users] About system requirement to gromacs

2012-08-01 Thread rama david
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

Re: [gmx-users] About system requirement to gromacs

2012-08-01 Thread Mark Abraham
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

Re: [gmx-users] About system requirement to gromacs

2012-08-01 Thread rama david
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

Re: [gmx-users] About system requirement to gromacs

2012-08-01 Thread Linus Östberg
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

Re: [gmx-users] About system requirement to gromacs

2012-08-01 Thread Mark Abraham
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

Re: [gmx-users] About system requirement to gromacs

2012-08-01 Thread rama david
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

Re: [gmx-users] About system requirement to gromacs

2012-08-01 Thread Mark Abraham
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