[gmx-users] mpi run in Gromacs

2011-03-02 Thread Selina Nawaz
Hi, I am a Phd student studying polymer membranes. I have installed Gromacs version 4.5.2 on our department cluster and attempted to run a simulations on a DPPC bilayer membranes taken from the tielleman website. I have set the system up in an NPT ensemble using a semi-isotropic pressure

Re: [gmx-users] mpi run in Gromacs

2011-03-02 Thread Erik Marklund
Selina Nawaz skrev 2011-03-02 11.54: Hi, I am a Phd student studying polymer membranes. I have installed Gromacs version 4.5.2 on our department cluster and attempted to run a simulations on a DPPC bilayer membranes taken from the tielleman website. I have set the system up in an NPT ensemble

Re: [gmx-users] mpi run in Gromacs

2011-03-02 Thread Mark Abraham
On 2/03/2011 11:37 PM, Erik Marklund wrote: Selina Nawaz skrev 2011-03-02 11.54: Hi, I am a Phd student studying polymer membranes. I have installed Gromacs version 4.5.2 on our department cluster and attempted to run a simulations on a DPPC bilayer membranes taken from the tielleman

[gmx-users] mpi run in Gromacs 4.5.3

2010-12-13 Thread Te, Jerez A., Ph.D.
Hi, I have been trying to run Gromacs 4.5.3 parallel simulations using openmpi 1.4.2. From my understanding, mdrun_mpi is not used in this version of Gromacs. Our system administrator told me that all mpi related options have been turned on while installing Gromacs. With either commands: mdrun

Re: [gmx-users] mpi run in Gromacs 4.5.3

2010-12-13 Thread Mark Abraham
On 14/12/2010 7:48 AM, Te, Jerez A., Ph.D. wrote: Hi, I have been trying to run Gromacs 4.5.3 parallel simulations using openmpi 1.4.2. From my understanding, mdrun_mpi is not used in this version of Gromacs. I don't understand what (you think) you mean. You can use thread-based

RE: [gmx-users] mpi run in Gromacs 4.5.3

2010-12-13 Thread Te, Jerez A., Ph.D.
: [gmx-users] mpi run in Gromacs 4.5.3 On 14/12/2010 7:48 AM, Te, Jerez A., Ph.D. wrote: Hi, I have been trying to run Gromacs 4.5.3 parallel simulations using openmpi 1.4.2. From my understanding, mdrun_mpi is not used in this version of Gromacs. I don't understand what (you think) you mean

Re: [gmx-users] mpi run in Gromacs 4.5.3

2010-12-13 Thread Justin A. Lemkul
option will be printed if you issue mdrun -h. -Justin Thanks, JT -Original Message- From: gmx-users-boun...@gromacs.org on behalf of Mark Abraham Sent: Mon 12/13/2010 4:38 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] mpi run in Gromacs 4.5.3 On 14/12/2010 7:48 AM, Te

Re: [gmx-users] mpi run in Gromacs 4.5.3

2010-12-13 Thread Mark Abraham
-configured MPI compiler and environment for it to work Mark Thanks, JT -Original Message- From: gmx-users-boun...@gromacs.org on behalf of Mark Abraham Sent: Mon 12/13/2010 4:38 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] mpi run in Gromacs 4.5.3 On 14/12/2010 7:48