Hello:
I've generate a .tpr file in my local machine and I am going to submit it
to different cluster. I am just wondering, will the trajectory exactly the
same?
thank you very much
albert
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Dear peers,
If I understand correctly, I can get the H-tide from the H (convered En.).
What I need to do is get the time intergration of dK (eq. 7 in jcp 2007), which
is the auxiliary dynamics.
But it not in a standard output. How can I get it ?
Can anyone help me ?
Many thanks!
wade
--
Hi,
I would like to redirect gromacs trajectories from one gmx module to another,
e.g. using a shell pipe...
For example, analyzing a trajectory which is split into two files could be done
using
gmx trjcat -f traj.part1.xtc traj.part2.xtc -o traj.cat.xtc gmx whatever -f
traj.cat.xtc -o result
I
Dear gromacs usres,
I want to run nvt simulation of water-ion cluster (Na+(H2O)250) in gas phase
(vacuum) at higher temperature ( bigger than 200 K).
But the cluster will collapse at high temperature. So the distance restraints
is used to restraint the water molecules and the ion Na+ not to
Thanks for you reply.
On a different machine I've recompiled GROMACS with icc version 13.1.0 (gcc
version 4.4.6 compatibility).
cmake command:
I_MPI_CC=nvcc CC=icc CXX=icpc cmake ../gromacs-src
-DCMAKE_INSTALL_PREFIX=~/gromacs-5.0.2/ -DGMX_FFT_LIBRARY=MKL -DGMX_MPI=OFF
-DGMX_GPU=OFF
Hi,
Very likely that simulation is too small to make good use of that many
cores (though if there's hyper-threading going on, then there may only be 8
real cores, and you may do better with hyper-threading off...). Gromacs use
of OpenMP does not do very well with lots of threads and few atoms. If
No. http://www.gromacs.org/Documentation/Terminology/Reproducibility
Mark
On Mon, Oct 13, 2014 at 8:32 AM, Albert mailmd2...@gmail.com wrote:
Hello:
I've generate a .tpr file in my local machine and I am going to submit it
to different cluster. I am just wondering, will the trajectory
Hi,
Unfortunately, Gromacs file handling wasn't designed with pipes in mind. In
particular, we often open a file, read its header to get some information,
and then go back and read the file again, which doesn't work well with
using pipes (see http://redmine.gromacs.org/issues/1489 for details).
What about trying a larger system, ~10,000 interaction centers?
The performance which you report is much below natural expectations for GROMACS.
Dr. Vitaly V. Chaban
Виталий Витальевич ЧАБАН
On Mon, Oct 13, 2014 at 10:55 AM, Олег Титов tito...@qsar.chem.msu.ru wrote:
Thanks for you reply.
Hi. Does that mean the umbrella don't overlap enough at those z ?
Can you make an overlay plot of the histograms of each umbrella?
On Mon, Oct 13, 2014 at 1:54 AM, Sathish Kumar sathishk...@gmail.com
wrote:
Dear gromacs usres,
I have run the umbrella sampling with the help of tutorial of
Yes, it means what you say.
I would decrease the number of bins.
Dr. Vitaly V. Chaban
Виталий Витальевич ЧАБАН
On Mon, Oct 13, 2014 at 12:47 PM, Johnny Lu johnny.lu...@gmail.com wrote:
Hi. Does that mean the umbrella don't overlap enough at those z ?
Can you make an overlay plot of the
On 10/13/14 4:48 AM, liuyong_1...@dicp.ac.cn wrote:
Dear gromacs usres,
I want to run nvt simulation of water-ion cluster (Na+(H2O)250) in gas phase
(vacuum) at higher temperature ( bigger than 200 K).
But the cluster will collapse at high temperature. So the distance restraints
is used to
On 10/13/14 8:17 AM, Nilesh Dhumal wrote:
Hello,
I am getting a following error for pdb2gmx.
Fatal error:
Atom O in residue BTC 1 not found in rtp entry with 156 atoms
while sorting atoms
Could anyone tell whats going wrong?
Atoms named O1 or O2 get translated per
OK, I think I get the right chemical potential.
Thank you for answer.
Regards,
QHwan
--
Kim Q Hwan
Center of Nano-Liquid
Department of Physics Astronomy
Seoul National University
Sent with Sparrow (http://www.sparrowmailapp.com/?sig)
On 2014년 10월 9일 Thursday at 오전 2:55, João M. Damas
On page 014101-3, the Bussi paper (http://dx.doi.org/10.1063/1.2408420)
mentioned: On the other hand, for coupling constant approaching
infinity,the Hamiltonian dynamics is recovered.
Does that means that for a large enough coupling constant, the velocities
are nearly not rescaled, and the
I guess, if I pick a coupling constant that is just small enough to keep the
energy conserved, I would get a NVT simulation that is as close as a NVE
simulation as possible.
Is this correct?
Yes, but then at that point the thermostat isn't actually thermostatting.
The Bussi comment is merely
Good day,
Here is the .log file
https://drive.google.com/file/d/0B3p_uIrSkPysS2kweC1QWUVfaTA
Regards
Oleg Titov
2014-10-13 13:31 GMT+04:00 Mark Abraham mark.j.abra...@gmail.com:
Hi,
Very likely that simulation is too small to make good use of that many
cores (though if there's
Hai
Yes, I have ploted the histogram, all windows are merged..please
check this histo.jpg file attached to the below link.
https://www.dropbox.com/s/ndl0w250dnawmib/histogram.jpg?dl=0
On Mon, Oct 13, 2014 at 3:47 AM, Johnny Lu johnny.lu...@gmail.com wrote:
Hi. Does that mean the
I am not able to find wheather the windows are overlaped or not. Please
help me in this.
Thanks.
On Mon, Oct 13, 2014 at 10:05 AM, Sathish Kumar sathishk...@gmail.com
wrote:
Hai
Yes, I have ploted the histogram, all windows are merged..please
check this histo.jpg file attached to the
On 10/13/14 1:08 PM, Sathish Kumar wrote:
I am not able to find wheather the windows are overlaped or not. Please
help me in this.
You've got a gap in the sampling exactly where g_wham tells you. The histograms
show this. You either need more windows or a different force constant, or
Hai
I have decreased the number of bins=50 and i have not get the
previously mentioned warnings. Still, the profile.xvg is looking like below
2.148184e+000.00e+00
2.300988e+000.00e+00
2.453792e+000.00e+00
2.606596e+000.00e+00
2.759400e+000.00e+00
Hi,
As the log file points out, you picked a combinations of settings that
do not have corresponding optimized non-bonded kernels:
LJ-PME with Lorentz-Berthelot is not supported with SIMD kernels,
falling back to plain-C kernels
Using plain C 4x4 non-bonded kernels
WARNING: Using the slow
I just want something that will patch up the energy lost due to numerical
error of NVE simulation of the system ran by mixed precision gromacs,
instead of a thermostat.
I hope the velocity rescaling is sufficiently uncorrelated with the motion
of the protein.
So far, the simulations ran 2.5 ns,
The simulation get worse in a new way.
I see that thermostat scales velocity and may not fix numerical error in
potential energy.
On Mon, Oct 13, 2014 at 2:07 PM, Johnny Lu johnny.lu...@gmail.com wrote:
I just want something that will patch up the energy lost due to numerical
error of NVE
Thank you, Szilárd, for this list of options!
2014-10-13 22:00 GMT+04:00 Szilárd Páll pall.szil...@gmail.com:
Hi,
As the log file points out, you picked a combinations of settings that
do not have corresponding optimized non-bonded kernels:
LJ-PME with Lorentz-Berthelot is not supported
Dear gmx user:
I got this error:Attempting to read a checkpoint file of version 15 with
code of version 12, when i'm running my simulation for npt process.
Anyone know how could i fix this and why does this happen?
I'm running my simulations at Gromacs 4.5.5.
Thank you very much!
Mengxue
--
On 10/13/14 8:50 PM, ookami a wrote:
Dear gmx user:
I got this error:Attempting to read a checkpoint file of version 15 with
code of version 12, when i'm running my simulation for npt process.
Anyone know how could i fix this and why does this happen?
I'm running my simulations at Gromacs
hello,
I running grompp for simulation. I get Segmentation fault error.
grompp -f 600.mdp -c cu.gro -p cu_btc_1.top -o 1.tpr
checking input for internal consistency...
processing topology...
Segmentation fault
Could any one tell what is the problem?
Thanks,
Nilesh
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Gromacs Users
hello gromacs user i am working on protein ligand complex with popc membrane
i am running production md in extended time (40 ns) i got some file i
am using -noappend option i got confout.gro file in each extended time
what is the use of this file if i want see my protein or ligand are in
proper
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