Dear users:
I am seeing a 140% performance boost when moving from gromacs 4.5.5 to 4.6.1
when I run a simulation on a single node. However, I am "only" seeing a 110%
performance boost when running on multiple nodes. Does anyone else see this?
Note that I am not using the verlet cutoff scheme.
DEAR ALL
For RDF calculation in invaccuo simulation I have given the
command as follows
./g_rdf_d -f outputdsvaccum_md.trr -s outputdsvaccum_md.tpr -n index.ndx
-nopbc -o rdfss.xvg
I am getting the graph which I have attached with this mail. Can you suggest
Dear users:
does anybody have any experience with gromacs on a cluster in which each node
is composed of 1 or 2 x86 processors plus an Intel Xeon Phi coprocessor? Can
gromacs make use of the xeon phi coprocessor? If not, does anybody know if that
is in the pipeline?
Thank you,
Chris.
--
gmx-us
Dear users,
I want to apply dihedral restraint and got everything set up in the topology
but I do not know the way to define the restraining force constant.
In the older grimaces versions one had the dihre_fc option but this is not
present in the 4.6 version.
I read a post on the user list abo
Dear users,
I used mkang_ndx to create an index file with dihedral angles.
Input was:
mk_angndx -s a.tpr -n angle.ndx -type dihedral
output angle.ndx read like this -
[ Phi=180.0_2_43.93 ]
52018192237353627323031
39595758
Hi Szilard
Thanks for this tip; it was extremely useful. The problem was indeed the
incompatibility between the installed NVIDIA driver and the CUDA 5.0
runtime library. Installation of an older driver solved the problem. The
programs devideQuery etc can now detect the GPU.
GROMACS can also detec
What output do you get from gmxcheck -f martin_md_290K_100ns_tau1.xtc ? Also,
can you extract that problematic frame with trjconv and run g_density on that
one frame (what happens?). Also, can you make a new .xtc that is missing that
last frame and see what g_density does?
These will help you t
Hi,
I would like to report a problem when trying to install gromacs-4.6.1 with
cmake together with QMMM orca interface.
My installation command is as follows:
CMAKE_INCLUDE_PATH=/opt/fftw/include CMAKE_LIBRARY_PATH=/opt/fftw/lib cmake ..
-DCMAKE_INSTALL_PREFIX=/opt/gmx-4.6.1_qmmm_orca -DGMX_QMM
Hi Reid,
Just saw your bug report and realized that you have an ancient kernel which
could be causing the issue. Let's move the discussion to the bug page (
http://redmine.gromacs.org/issues/1184), hopefully we can narrow the issue
down and then post the conclusions to the list later.
Cheers,
--
Thank you for your answer.
I had tried to change the names before, but the error was then that the
atoms were not recognized. Reading your answer made me realize that I had
not gone far enough,
The solution I found is to create a residue in the .rtp that has the same
features as the terminal AA,
Thank you all. I found that in my ffbonded.itp I had the same lines
with other values. I used the new one produced by the newest version
of paramchem blocking the old one. It works now.
Steven
On Thu, Mar 7, 2013 at 10:24 PM, Baptiste Demoulin
wrote:
> Hello Steven,
>
> I would suggest you to lo
Hi All
I have a 100 ns lipid simulation for which I want the density profile. I
issued the following command
g_density -f martin_md_290K_100ns_tau1.xtc -n dppc.ndx -s
martin_md_290K_100ns_tau1.tpr -o water_density.xvg -b 5
The program fails with the following message
Selected 3: 'Water'
Last
Great -- if it doesn't seem to be working the way it should after some
playing around, then submit it as a redmine issue, and I'll take a
look.
On Fri, Mar 8, 2013 at 2:51 AM, Joakim Jämbeck wrote:
> Dear Michael,
>
> Thank you for your reply.
>
> Yes, it is relatively clear now. Will try to play
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