Hey GROMACS users,
using mdrun (version 4.6-beta3) on a GPU node (1 nvidia K10 with cuda
drivers and runtime 4.2 + 2 times intel 6 core E5 with hyper threading
and SSE4.1) I get allways after a few or few 100 ns the following segfault:
line 15: 28957 Segmentation fault mdrun -deffnm
Dear Gromacs Users!
I'd like to know if it's possible to obtain some values from do_dssp
except the graph diagrams of the ss dynamics ? For example I wounder
to know values of how many residues were in helix, sheet or coil
conformation during my simulation ?
By the way during analysis of the
Dear users,
I usually apply the positions restraint of 100 ps on system. Does it
produce a problem to apply the positions restraint for long time (100 or
200 ps)? cant it cause strain on structure?
Thanks in advance
--
Ahmet Yıldırım
--
gmx-users mailing listgmx-users@gromacs.org
On Mon, Jan 14, 2013 at 9:23 PM, santhosh mesan...@gmail.com wrote:
I want to output pdb during the run. Before every integration step, I want
to output the current configuration of the system.
Before an integration step is after the previous integration step,
which is where the normal
On 1/15/13 3:19 AM, James Starlight wrote:
Dear Gromacs Users!
I'd like to know if it's possible to obtain some values from do_dssp
except the graph diagrams of the ss dynamics ? For example I wounder
to know values of how many residues were in helix, sheet or coil
conformation during my
On 1/15/13 3:28 AM, Ahmet yıldırım wrote:
Dear users,
I usually apply the positions restraint of 100 ps on system. Does it
produce a problem to apply the positions restraint for long time (100 or
200 ps)? cant it cause strain on structure?
Unlikely. The amount of equilibration necessary
On 1/15/13 5:49 AM, Devika N T wrote:
HI
I would like to know the protocol to be followed for performing MD
simulation
for calcium with protein (Calmodulin)
Can I follow the same protocol which is followed for a protein?
Probably, as long as the force field you choose can deal with
Hi,
I'm seeing MD simulation running a lot slower with the sd integrator than with
md - ca. 10 vs. 30 ns/day for my 47000 atom system. I found no documented
indication that this should be the case.
Timings and logs pasted in below - wall time seems to be accumulating up in
Update and Rest,
On 1/15/13 7:06 AM, Dr. Vitaly Chaban wrote:
using mdrun (version 4.6-beta3) on a GPU node (1 nvidia K10 with cuda
drivers and runtime 4.2 + 2 times intel 6 core E5 with hyper threading
and SSE4.1) I get allways after a few or few 100 ns the following segfault:
line 15: 28957 Segmentation
Justin,
I want to obtain timescale on X as well as number of residues on Y
on the xmp graph . By default that graph has not legend so it's hard
to analyse it .
By the way have you forced with some problems with dppc ? Simetimes
I've obtain error like
There are 286 residues in your selected
On 01/15/2013 01:09 PM, Justin Lemkul wrote:
On 1/15/13 7:06 AM, Dr. Vitaly Chaban wrote:
using mdrun (version 4.6-beta3) on a GPU node (1 nvidia K10 with cuda
drivers and runtime 4.2 + 2 times intel 6 core E5 with hyper threading
and SSE4.1) I get allways after a few or few 100 ns the
On Tue, Jan 15, 2013 at 1:09 PM, Justin Lemkul jalem...@vt.edu wrote:
On 1/15/13 7:06 AM, Dr. Vitaly Chaban wrote:
using mdrun (version 4.6-beta3) on a GPU node (1 nvidia K10 with cuda
drivers and runtime 4.2 + 2 times intel 6 core E5 with hyper threading
and SSE4.1) I get allways after a
On 1/15/13 7:13 AM, James Starlight wrote:
Justin,
I want to obtain timescale on X as well as number of residues on Y
on the xmp graph . By default that graph has not legend so it's hard
to analyse it .
The legends are printed in the .xvg header. I've never had a problem plotting
On 1/15/13 7:16 AM, Dr. Vitaly Chaban wrote:
On Tue, Jan 15, 2013 at 1:09 PM, Justin Lemkul jalem...@vt.edu wrote:
On 1/15/13 7:06 AM, Dr. Vitaly Chaban wrote:
using mdrun (version 4.6-beta3) on a GPU node (1 nvidia K10 with cuda
drivers and runtime 4.2 + 2 times intel 6 core E5 with
On Tue, Jan 15, 2013 at 1:09 PM, Justin Lemkul jalem...@vt.edu wrote:
On 1/15/13 7:06 AM, Dr. Vitaly Chaban wrote:
using mdrun (version 4.6-beta3) on a GPU node (1 nvidia K10 with cuda
drivers and runtime 4.2 + 2 times intel 6 core E5 with hyper threading
and SSE4.1) I get allways after a
Am 15.01.2013 12:52, schrieb gmx-users-requ...@gromacs.org:
On 1/15/13 5:49 AM, Devika N T wrote:
HI
I would like to know the protocol to be followed for performing MD
simulation
for calcium with protein (Calmodulin)
Can I follow the same protocol which is followed for a protein?
Probably,
On 1/15/13 8:12 AM, Thomas Schlesier wrote:
Am 15.01.2013 12:52, schrieb gmx-users-requ...@gromacs.org:
On 1/15/13 5:49 AM, Devika N T wrote:
HI
I would like to know the protocol to be followed for performing MD
simulation
for calcium with protein (Calmodulin)
Can I follow the same
Am 15.01.2013 14:17, schrieb gmx-users-requ...@gromacs.org:
On 1/15/13 8:12 AM, Thomas Schlesier wrote:
Am 15.01.2013 12:52, schriebgmx-users-requ...@gromacs.org:
On 1/15/13 5:49 AM, Devika N T wrote:
HI
I would like to know the protocol to be followed for performing MD
simulation
for
Justin, thanks both options works perfect.
James
2013/1/15 Justin Lemkul jalem...@vt.edu:
On 1/15/13 7:13 AM, James Starlight wrote:
Justin,
I want to obtain timescale on X as well as number of residues on Y
on the xmp graph . By default that graph has not legend so it's hard
to
Restating of my question about ussage of essential eigenvectors as the
pulling coordinates I'd like to introduce some example.
The case study is the open to close transition in some protein. For
instance by means of essential dynamics sampling technique (in
targeted-contraction mode) I've
@Bogdan : It differs from the normal gromacs setup as this PDB write is
expected to happen during the run. (While the simulation is still running).
I have posted this in gmx-developers post as I felt its more apt after
Justins advice.
--
View this message in context:
Dear All,
I've just installed 4.6-beta3 on my ubuntu linux (Intel Xeon [sandy
bridge]) box using both intel-suite/64/2011.10/319, and
intel-suite/64/2013.0/079 with mkl
Using either compiler I received several hundred warnings of type #120,
#167, and #556 (see bellow for examples). I
Hi,
Please try to run the very same simulation that crashes on CPUs only (-nb
cpu). If that also crashes, please file a bug report because we surely have
a software bug.
If that does not crash, we will have to dig a bit deeper into what could be
causing the issue.
Log files from the two runs
Hi Floris,
Great feedback, this needs to be looked into. Could you please file a bug
report, preferably with a tpr (and/or all inputs) as well as log files.
Thanks,
--
Szilárd
On Tue, Jan 15, 2013 at 3:50 AM, Floris Buelens floris_buel...@yahoo.comwrote:
Hi,
I'm seeing MD simulation
Hi,
could you check if you get these warnings also with the latest version from
git? We have changed quite a bit sense then.
git clone https://gerrit.gromacs.org/p/gromacs
git checkout release-4-6
Roland
On Tue, Jan 15, 2013 at 9:34 AM, Richard Broadbent
richard.broadben...@imperial.ac.uk
Maybe a somewhat dumb question:
How do forces from PME get calculated?
In the manual (and also some textbooks) i have only found expressions for the
potential for PME (or ewald-summation), but no information how the forces get
calculated.
One idea i have would be
dF_i = - [ V(r_i(t)) -
Hi gmx users, I'm writing a MD code and, comparing with gromacs, I have
some doubts. When I put gen-pairs=yes, fudges=0.5 and no [pairs] or
[pairtypes] directives, the program (gmx) would generate 1,4 pairs with the
parameters described in the [atomtypes] directive, right? But, at the end
of the
Hi Thomas,
There are different possibilities to derive the forces from the PME method.
Usually with SPME, the so called analytical differentiation scheme is
applied, where the gradient of the reciprocal sum is directly calculated.
This is computationally very efficient, because it requires only
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