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
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/
;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 :
>
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
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
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
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,
>>
>&
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
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
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
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
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
--
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
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