Dear all,
We have installed the latest version of Gromacs (version 4.6) on our
cluster by the following step:
* cmake .. -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/backup/sicnas/gromacs
-DGMX_BUILD_OWN_FFTW=ON -DGMX_PREFER_STATIC_LIBS=ON
The interconnection of the cluster is Myrinet2000 and
Hi, see installation instruction with CMAKE here:
http://www.gromacs.org/Documentation/Installation_Instructions
I guess that maybe you need to specify your Openmpi and FFTW installation
directories using options CMAKE_PREFIX_PATH.
For example, my Openmpi and FFTW were firstly installed in
Hello:
I've got two GPU workstation both of which have two GTX690 GPU. Now
I am planning to run Gromacs GPU version and I am just wondering can we
submit a single GPU jobs in one machine and evoke all GPU resources from
both machine?
thank you very much
best
Albert
--
gmx-users mailing
Dear all,
Due to cluster wall-time limitations, I was forced to restart two REMD
simulations. It ran absolutely fine until hitting the wall-time. To restart
I used the following command:
mpirun -np 64 -output-filename MPIoutput $GromDir/mdrun_mpi -s H5_.tpr
-multi 64 -replex 1000 -deffnm H5_
Dear Zhikun Cai,
Thank you for your quick response.
On 4/8/13 11:15 AM, Zhikun Cai wrote:
Hi, see installation instruction with CMAKE here:
http://www.gromacs.org/Documentation/Installation_Instructions
I guess that maybe you need to specify your Openmpi and FFTW installation
directories
Hi, is it possible to instruct gromacs to only perform the dynamics on
half of the system or protein while ignoring the rest?
thanks
Would you explain to us why you need so exotic setup?
Dr. Vitaly Chaban
--
gmx-users mailing listgmx-users@gromacs.org
I've got two GPU workstation both of which have two GTX690 GPU. Now
I am planning to run Gromacs GPU version and I am just wondering can we
submit a single GPU jobs in one machine and evoke all GPU resources from
both machine?
If I were you, I would insert both cards into the same
Dear GROMACS user,
Last week I was watching the GTC talk from Eric Lindahl, and I noticed his
insistence on virtual site to accelerate simulation (up to 5ps time step).
As a matter of fact our group recently tried to use virtual site on CHARMM36
POPC bilayer and the result where less than
Sure, it's basically improving minimization time. if i can focus all my
resources in simulating or minimizing a portion of the system while ignoring
other parts that are too far away from the selected portion, it can also be
possible to run some simulations without the need of a big cluster and
On 2013-04-08 11:34, Bastien Loubet wrote:
Dear GROMACS user,
Last week I was watching the GTC talk from Eric Lindahl, and I noticed his
insistence on virtual site to accelerate simulation (up to 5ps time step).
As a matter of fact our group recently tried to use virtual site on CHARMM36
POPC
I thought the sole purpose of open source discussions and sharing is to
help any scientific (or other) community to grow and benefit from each
other, without taking into account the Nationality of the beneficiaries. If
someone is willingly helping out somebody, whether Indian or not, in the
If you do not care about the atoms, which are too far away from the region
of interest, is it not reasonable just to cut that useless part? Also,
you may want to look towards implicit solvent simulations.
Dr. Vitaly Chaban
On Mon, Apr 8, 2013 at 11:35 AM, Juan Antonio Raygoza Garay
On 2013-04-08 11:52, David van der Spoel wrote:
On 2013-04-08 11:34, Bastien Loubet wrote:
Dear GROMACS user,
Last week I was watching the GTC talk from Eric Lindahl, and I noticed
his
insistence on virtual site to accelerate simulation (up to 5ps time
step).
As a matter of fact our group
Sir
I was using an old version. Now I used 4.5.5, it still gives me the same
blank output file.
Kindly suggest how to go about solving this
Thanks
On Sat, Apr 6, 2013 at 2:26 PM, Mark Abraham mark.j.abra...@gmail.comwrote:
On Sat, Apr 6, 2013 at 7:19 AM, Venkat Reddy venkat...@gmail.com
Dear Qinghua Liao -
In that case, I am just wishing you luck with the copper containing systems.
Are you going to simulate copper-ligand interactions using Coulomb+LJ
potential only? I would guess it is a chemical bonding case. Maybe the
Morse potential (additionally) can be of better service?
hello,
I have a protein in which I fixed Xenon in the binding sites. without
xenon, I used GROMOS96 53a6 force field for simulation. With Xenon, which
forcefield am I able to use?
thanking you
regards
Divya
--
gmx-users mailing listgmx-users@gromacs.org
On Mon, Apr 8, 2013 at 2:28 AM, Hrachya Astsatryan hr...@sci.am wrote:
Dear all,
We have installed the latest version of Gromacs (version 4.6) on our
cluster by the following step:
* cmake .. -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/**backup/sicnas/gromacs
-DGMX_BUILD_OWN_FFTW=ON
On Mon, Apr 8, 2013 at 5:04 PM, Divya Sunil divyasunilku...@gmail.comwrote:
hello,
I have a protein in which I fixed Xenon in the binding sites. without
xenon, I used GROMOS96 53a6 force field for simulation. With Xenon, which
forcefield am I able to use?
Xenon is a non-standard molecule
On Mon, Apr 8, 2013 at 5:54 AM, Dr. Vitaly Chaban vvcha...@gmail.comwrote:
If you do not care about the atoms, which are too far away from the region
of interest, is it not reasonable just to cut that useless part? Also,
Hear hear. If it's so meaningless, why is it there? ;)
you may want
In literature I found that the ussage of 1.0 cutoffs should give good
results but in the antechamber manual I've seen that usages of 1.2 cutoofs
( with GAFF) should be used. So what cut-offs should I use for
protein-ligand complexes done in amber ? (assuming that I simulate my
system in the berger
I believe the problem is in the way which you used to convert AMBER
trajectory to the GROMACS trajectory
I would suggest to try gmxdump and see what your trajectory looks like. Oe
maybe even better - try to visualize it in VMD to see if the format is
correct.
Dr. Vitaly Chaban
Sir
I was
Actually we did not increase the time step between the simulations. The plan
was to increase it after we checked the basic properties of the membrane,
but we never got to that point.
I will try to put something together for redmine soon.
Thanks for the answer,
Bastien
--
View this message in
You might use freeze groups or position restraints depending what you want.
See manual.
Mark
On Apr 8, 2013 2:58 AM, Juan Antonio Raygoza Garay raygo...@psu.edu
wrote:
Hi, is it possible to instruct gromacs to only perform the dynamics on
half of the system or protein while ignoring the rest?
Yes, there's no way to cheat on the explicit electrostatics to reduce cost,
except implicit solvation. The kind of approach used in QM/MM is not useful
for MM/MM! The rate-limiting part is still there.
Mark
On Apr 8, 2013 12:42 PM, Justin Lemkul jalem...@vt.edu wrote:
On Mon, Apr 8, 2013 at
Dear All,
I tried to use g_clustsize_d program for estimation of temperature of
cluster/nanodroplet but the temperature output file is empty. Could you
comment where is the problem?
Please note that I can get Temperature of system using g_energy_d but I'm
interest to know cooling effect of
On Mon, Apr 8, 2013 at 9:01 AM, Rasoul Nasiri nasiri1...@gmail.com wrote:
Dear All,
I tried to use g_clustsize_d program for estimation of temperature of
cluster/nanodroplet but the temperature output file is empty. Could you
comment where is the problem?
Not without seeing your command
Bellow is my command which I used:
g_clustsize_d -f traj.xtc -s topol.tpr -n n.ndx -nc nclust.xvg -mc maxclust
.xvg -ac avclust.xvg -mcn maxclust.ndx -cut 0.516 -temp Tempe.xvg
Rasoul
On Mon, Apr 8, 2013 at 2:04 PM, Justin Lemkul jalem...@vt.edu wrote:
On Mon, Apr 8, 2013 at 9:01 AM, Rasoul
On Mon, Apr 8, 2013 at 9:08 AM, Rasoul Nasiri nasiri1...@gmail.com wrote:
Bellow is my command which I used:
g_clustsize_d -f traj.xtc -s topol.tpr -n n.ndx -nc nclust.xvg -mc
maxclust
.xvg -ac avclust.xvg -mcn maxclust.ndx -cut 0.516 -temp Tempe.xvg
Then it is exactly what I said.
On Mon, Apr 8, 2013 at 7:50 AM, James Starlight jmsstarli...@gmail.comwrote:
In literature I found that the ussage of 1.0 cutoffs should give good
results but in the antechamber manual I've seen that usages of 1.2 cutoofs
( with GAFF) should be used. So what cut-offs should I use for
Dear Dr. Vitaly Chaban,
Thanks very much for concern on my research! We are going to the use the
bonded model together with Coulomb and LJ potentials.
My problem is that vdw radius and its sigma do not follow the equation
of Rvdw = pow(2, 1/6)*sigma in the OPLS force field files,
not just
On Apr 8, 2013 8:53 AM, João Henriques joao.henriques.32...@gmail.com
wrote:
Dear all,
Due to cluster wall-time limitations, I was forced to restart two REMD
simulations. It ran absolutely fine until hitting the wall-time. To
restart
I used the following command:
mpirun -np 64
I think your misunderstanding comes from the belief that sigma (as they are
tabulated in the force field files) should *exactly correspond* to the VDW
diameter, as in encyclopedia.
This is simply not the case. In reality, sigmas in the force fields are
tuned in order to give right interatomic
Thank you very much. I didn't notice it until now considering all those
numbers look so similar. Great eye for detail!
João
On Mon, Apr 8, 2013 at 3:17 PM, Mark Abraham mark.j.abra...@gmail.comwrote:
On Apr 8, 2013 8:53 AM, João Henriques joao.henriques.32...@gmail.com
wrote:
Dear all,
Justin,
Thanks for your comment.
Instead of .xtc, I just used .trr in which nstvout isn’t zero. I'm still
encountering to empty file for temperature.
Rasoul
On Mon, Apr 8, 2013 at 2:10 PM, Justin Lemkul jalem...@vt.edu wrote:
On Mon, Apr 8, 2013 at 9:08 AM, Rasoul Nasiri nasiri1...@gmail.com
On Mon, Apr 8, 2013 at 9:24 AM, Rasoul Nasiri nasiri1...@gmail.com wrote:
Justin,
Thanks for your comment.
Instead of .xtc, I just used .trr in which nstvout isn’t zero. I'm still
encountering to empty file for temperature.
Can you please provide the gmxcheck output for the .trr file? I
Dear Dr. Vitaly Chaban,
Thanks very much for your patient explanation. Yeah, you are right, that
is what I want to know: how you tuned this parameter?
Since then, if I want to set a new atom type and I know its vdw radius,
so how should I set the sigma for it based on the vdw radius,
which
One suggestion,
Is there any chance to retrieve trajectory of un-evaporated molecules using
one of gromacs tools? Now I have a ndx file which show number of atoms
stayed in drop,
Which one is better? I mean if I can get trajectory (position+velocity)
unevaporated molecules, I would be able
On Mon, Apr 8, 2013 at 9:39 AM, Rasoul Nasiri nasiri1...@gmail.com wrote:
One suggestion,
Is there any chance to retrieve trajectory of un-evaporated molecules using
one of gromacs tools? Now I have a ndx file which show number of atoms
stayed in drop,
Sure, that's what trjconv does.
These are almost irrelevant for performance. What are you actually
simulating on what?
Mark
On Apr 7, 2013 2:12 AM, 陈照云 chenzhaoyu...@gmail.com wrote:
Hi!
I have 6 nodes. Each node has two CPUs,12 cores totally.
How should I set the options like -rdd,-rcon,-dds,-gcom to improve the
Funny, I thought of a large Ribosome system. You can in vacuo already with an i7 or AMD equivalent EM a 600 amino acid system with a 12-15A solvent shell in an hour to three using the CPU alone. Thats from test of Gromacs and a non-eqd system. so about 1 work day to get through NPT. Thus, I doubt
On Mon, Apr 8, 2013 at 3:36 PM, fantasticqhl fantastic...@gmail.com wrote:
Dear Dr. Vitaly Chaban,
Thanks very much for your patient explanation. Yeah, you are right, that
is what I want to know: how you tuned this parameter?
Since then, if I want to set a new atom type and I know its vdw
On Mon, Apr 8, 2013 at 1:37 PM, Justin Lemkul jalem...@vt.edu wrote:
On Mon, Apr 8, 2013 at 2:28 AM, Hrachya Astsatryan hr...@sci.am wrote:
Dear all,
We have installed the latest version of Gromacs (version 4.6) on our
cluster by the following step:
* cmake .. -DGMX_MPI=ON
I have recently installed version 4.6.1. The installation was successful with
all of the prerequisites, however mdrun tells me that the Quadro FX 5800 is
incompatible even though it is listed on the site as compatible.
1 GPU detected:
#0: NVIDIA Quadro FX 5800, compute cap.: 1.3, ECC: no,
On Mon, Apr 8, 2013 at 10:40 AM, bv07ay bv0...@brocku.ca wrote:
I have recently installed version 4.6.1. The installation was successful
with
all of the prerequisites, however mdrun tells me that the Quadro FX 5800 is
incompatible even though it is listed on the site as compatible.
1 GPU
Hello,
I am calculating the hydrogen bond life time for my system, ionic liquids.
I am calculating the hydrogen bond life time using g_hbond in Groamcs.
Attached the plot p(t)vs time and the exponential decay is not sooth.
Can you tell why is there is lot of noise.
Nilesh
--
gmx-users
Sir
I loaded the trajectory. There doesn't seem to be anything wrong with it.
Have no clue whats going wrong
Thanks
On Mon, Apr 8, 2013 at 5:28 PM, Dr. Vitaly Chaban vvcha...@gmail.comwrote:
I believe the problem is in the way which you used to convert AMBER
trajectory to the GROMACS
Do you experience this problem with g_rdf only, or with all gromacs
analysis utilities?
On Mon, Apr 8, 2013 at 7:33 PM, Venkat Reddy venkat...@gmail.com wrote:
Sir
I loaded the trajectory. There doesn't seem to be anything wrong with it.
Have no clue whats going wrong
Thanks
On Mon,
Dear all
I am simulating gold nanoparticle interaction with 10 aminoacids.Two amino
acids have been far from the nanoparticleafter 2000 steps.
Now, Can I change after2000 steps, the position of these 2 aminoacids in PDP
file and then continue the simulation?
Fatemeh Ramezani
--
gmx-users
On Mon, Apr 8, 2013 at 2:00 PM, fatemeh ramezani fr_...@yahoo.com wrote:
Dear all
I am simulating gold nanoparticle interaction with 10 aminoacids.Two
amino acids have been far from the nanoparticleafter 2000 steps.
Now, Can I change after2000 steps, the position of these 2 aminoacids in
It helped that I *really* knew one must differ ;-)
Mark
On Apr 8, 2013 2:24 PM, João Henriques joao.henriques.32...@gmail.com
wrote:
Thank you very much. I didn't notice it until now considering all those
numbers look so similar. Great eye for detail!
João
On Mon, Apr 8, 2013 at 3:17 PM,
Sorry, I tried posting this once but it was spammed or something. In any case, are there any suggestions for mostly MD based journals (publication wise as content), a favorites or something if somone wanted to turn it into that,
Stephan Watkins
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gmx-users mailing list
Hi!
I'm interested in using CHARMM's General Force Field for organic molecules
(CGenFF) in Gromacs.
For that, I've downloaded the files top_all36_cgenff.rtf,
par_all36_cgenff.prm (from http://mackerell.umaryland.edu/~kenno/cgenff/)
which, correspond to the topology and parameters files
On Mon, Apr 8, 2013 at 7:56 PM, jbermudez bto89meis...@gmail.com wrote:
Hi!
I'm interested in using CHARMM's General Force Field for organic molecules
(CGenFF) in Gromacs.
For that, I've downloaded the files top_all36_cgenff.rtf,
par_all36_cgenff.prm (from
Hi!
I want to improve my mdrun performance with k20.But there is something
wrong.
My gromacs version is 4.6.1. My openmm version is 5.0.1. The wrong
message is include could not find load file: ../contrib/BuildMdrunOpenMM
Can the openmm version match k20?
Thanks!
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gmx-users mailing
On Mon, Apr 8, 2013 at 8:58 PM, 陈照云 chenzhaoyu...@gmail.com wrote:
Hi!
I want to improve my mdrun performance with k20.But there is something
wrong.
My gromacs version is 4.6.1. My openmm version is 5.0.1. The wrong
message is include could not find load file:
Sir
I tried g_msd, after asking for group selection the program appears not to
read the frames as it remains stuck at reading frame 0, time 0.00.
What to do?
Thanks
On Mon, Apr 8, 2013 at 11:16 PM, Dr. Vitaly Chaban vvcha...@gmail.comwrote:
Do you experience this problem with g_rdf only,
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