[gmx-users] average pressure using g_energy

Hi, We have run an NPT equilibration on a protein embedded in a membrane and calculated the average pressure using g_energy. We then imported the resulting xvg file into excel and recalculated the average. The 2 numbers differed. Specifically, the gromacs average pressure was 0.942858 while t

[gmx-users] Installing GMX-GPU 4.5.5

Hi, I'm compiling gromacs 4.5.5 with gcc compiler (v 4.5.3), cmake (2.8.7) and OpenMM 3.1.1 on Linux (Red Hat release 5.7). I have followed the installation instructions. The configuration seems to work well. > ~/progs/cmake-2.8.7/bin/cmake -DGMX_OPENMM=ON > -DCUDA_TOOLKIT_ROOT_DIR:PATH=/opt/

[gmx-users] Installing GMX-GPU 4.5.5

;Subject: Re: [gmx-users] Installing GMX-GPU 4.5.5 >To: Discussion list for GROMACS users >Message-ID: >Content-Type: text/plain; charset=UTF-8 >You should try this: >http://verahill.blogspot.com/2012/01/debian-testing-64-wheezy-compiling_20.html >2012/1/31 Efrat Exlrod : >

[gmx-users] Gromacs-GPU benchmark test killed after exhausting the memory

Hi, I have Gromacs- GPU version 4.5.5 and GTX 580. I run dhfr-solv-PME benchmark test (see below) and my run is killed after couple of hours when it exhausts all the computer memory, including the swap (2G + 4G swap). Has anyone encountered this problem? What do I do wrong? Thanks, Efrat -- gm

[gmx-users] FW: Gromacs-GPU benchmark test killed after exhausting the memory

d ____ From: Efrat Exlrod Sent: Monday, February 20, 2012 11:33 AM To: gmx-users@gromacs.org Subject: Gromacs-GPU benchmark test killed after exhausting the memory Hi, I have Gromacs- GPU version 4.5.5 and GTX 580. I run dhfr-solv-PME benchmark test (see below) and my r

[gmx-users] Gromacs-GPU benchmark test killed after exhausting the memory

Hi, I have Gromacs-GPU version 4.5.5 and GTX 580. I ran dhfr-solv-PME benchmark test (see below) and my run was killed after couple of hours exhausting all the computer memory, including the swap (2G + 4G swap). Has anyone encountered this problem? What is wrong? Thanks, Efrat > mdrun-gpu -dev

[gmx-users] Re: Gromacs-GPU benchmark test killed after exhausting the memory

hange whatsoever (see the plot >attached). > >I've attached a script I used to monitor the memory usage, feel free >to use if you want check again. > >Cheers, >-- >Szil?rd > > > >On Wed, Feb 29, 2012 at 9:50 AM, Efrat Exlrod wrote: >> Hi, >> >&

[gmx-users] Gromacs on GPU: GTX or Tesla?

Hi, We want to start using Gromacs on GPU and we are debating whether to purchase GeForce GTX card or Tesla platform. Looking at the published data it seems GTX580 has much impressive performance compared to Tesla C2050, and of course it is much cheaper. Is there a reason to prefer Tesla over

[gmx-users] RE: Gromacs on GPU: GTX or Tesla?

Hi Szilard, Thank you very much for your input. At the moment we want to buy a single card (GTX-580?) in order to gain experience in working with GPUs. In the future we will probably like to have a cluster, especially when multiple GPU cards will be supported by Gromacs. Thanks, Efrat D

[gmx-users] setting working directory

Hi There! Is it possible to run mdrun from a shared directory and set the working directory to a local directory on the computer on which it runs, in order to decrease NFS load? Thanks, Efrat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-u

[gmx-users] gromacs 4.5.3 and GCC 4.1.x

Hi, I want to install standard gromacs 4.5.5 on a new linux machine, prior to installing GPU accelerated gromacs. Looking at the installation instructions I see you recommend not to use GCC 4.1.x series of compilers. A year ago I have installed gromacs 4.5.3 and I don't recall seeing the r

[gmx-users] problem installing gromacs

Hi everyone, I have installed Gromacs 4.5.5 following the online installation guide without and with mpi. My configure lines (after few tries) were: ./configure CC=/private/gnss/local/bin/gcc CXX=/private/gnss/local/bin/g++ --prefix=/private/gnss/Gromacs_455 --disable-float --with-fft=fftw3 --

[gmx-users] trjconv -pbc mol/nojump

Hi, I have run simulation of a large solute in a box of water. Trying to look at the simulation output I used trjconv with and without the -pbc nojump option. For example: (1) trjconv_d -s md_100ns.tpr -f md_100ns.xtc -o md_100ns_noPBC_pbcmol.pdb -pbc mol -ur compact (2) trjconv_d -s md