1.- You can only run the MD part in 1 thread, but you can perform the QM
step with more procs. Note that, except for MOPAC, for which the library
libmopac (see instructions in the website for how to get this) is
directly used by the GROMACS code, the QM part consists in a external
call to the
Dear Javier;
Thanks for comprehensive explanations for elusive part of QM/MM
calculations.
Best Regards,
semran
2013/7/19 Javier Cerezo
>
> 1.- You can only run the MD part in 1 thread, but you can perform the QM
> step with more procs. Note that, except for MOPAC, for which the library
> l
According to the suggestion I added the box to the trajectory using -box
option of trjconv, using the following commands:
trjconv -f traj.xtc -s md.tpr -box 0.9 0.9 0.9 -o traj_box.xtc
then using the g_hbond on the output trjectory (traj_box.xtc) run
successfully but gives the wrong number of H-b
On 7/19/13 4:17 AM, bipin singh wrote:
According to the suggestion I added the box to the trajectory using -box
option of trjconv, using the following commands:
trjconv -f traj.xtc -s md.tpr -box 0.9 0.9 0.9 -o traj_box.xtc
then using the g_hbond on the output trjectory (traj_box.xtc) run
suc
I thought about this reguaring solvation energy. If you use a good water model, and make a secoundary index for solvent (ie Solvent2 atoms x-xn), the normal Gromacs energy extraction would allow you to just extract all energy between protein and solvent2. I assume you could do some extreemly a
Sorry for my silly mistake.
I have a doubt regarding the expected difference in total No. of H-bonds
calculated with whole a MD trajectory (protein+solvent box) and H-bonds
calculated with concatenated frames (only protein) from a MD trajectory.
I mean, will the number of H-bonds present at a pa
Hi
I am having problems creating static versions of the GROMACS binaries
for a Cray XE6 (www.hector.ac.uk). The build process I am using is
documented at:
http://www.hector.ac.uk/support/documentation/software/gromacs/compiling_4-6-1_phase3.php
and successfully produced static binaries for
What does build_*/src/buildinfo.h have to say about the compiler flags
that are getting used?
Mark
On Fri, Jul 19, 2013 at 12:55 PM, Andrew R Turner
wrote:
> Hi
>
> I am having problems creating static versions of the GROMACS binaries for a
> Cray XE6 (www.hector.ac.uk). The build process I am u
What's the simplest case you can make work?
Mark
On Fri, Jul 19, 2013 at 8:38 AM, Éric Germaneau wrote:
> I actually submitted using two MPI process per node but log files do not
> get updated, it's like the calculation gets stuck.
>
> Here is how I proceed:
>
>mpirun -np $NM -machinefile n
Hi Mark,
What does build_*/src/buildinfo.h have to say about the compiler flags
that are getting used?
/** C compiler flags used to build */
#define BUILD_CFLAGS"-msse2-Wextra
-Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused
-Wunused-value -static -O3 -
On 7/19/13 6:55 AM, bipin singh wrote:
Sorry for my silly mistake.
I have a doubt regarding the expected difference in total No. of H-bonds
calculated with whole a MD trajectory (protein+solvent box) and H-bonds
calculated with concatenated frames (only protein) from a MD trajectory.
I mean
Dear gmx users
I scrap lines from some files in oplsaa.ff folder as the following
ffnonbonded file:
[ atomtypes ]
opls_157 CT6 12.01100 0.145 A3.5e-01
2.76144e-01
atomtypes.atp file:
opls_157 12.01100 ; all-atom C: CH3 & CH2, alcohols
also, I looked at /groma
On 7/19/13 8:20 AM, afsaneh maleki wrote:
Dear gmx users
I scrap lines from some files in oplsaa.ff folder as the following
ffnonbonded file:
[ atomtypes ]
opls_157 CT6 12.01100 0.145 A3.5e-01
2.76144e-01
atomtypes.atp file:
opls_157 12.01100 ; all-atom C
Dear Justin
I want a topology for an arbitrary molecule (44 atom) and I use x2top
program that .n2t file is it’s input.
The .pdb file is as the following:
ATOM 1 O5 TPT 1 -6.131 -0.245 0.000 0.00
ATOM 2 C21 TPT 1 -5.041 0.384 0.000 0.00
ATOM
Depending on the level of parallelization (number of nodes and number
of particles/core) you may want to try:
- 2 ranks/node: 8 cores + 1 GPU, no separate PME (default):
mpirun -np 2*Nnodes mdrun_mpi [-gpu_id 01 -npme 0]
- 4 ranks per node: 4 cores + 1 GPU (shared between two ranks), no separat
On 7/19/13 8:53 AM, afsaneh maleki wrote:
Dear Justin
I want a topology for an arbitrary molecule (44 atom) and I use x2top
program that .n2t file is it’s input.
The .pdb file is as the following:
ATOM 1 O5 TPT 1 -6.131 -0.245 0.000 0.00
ATOM 2 C21 TPT
Dear Justin
thanks for your reply,
I did it. when I put the .n2t in my working directory,I have gotten this
error.
thanks in advance,
Afsaneh
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On 7/19/13 9:10 AM, afsaneh maleki wrote:
Dear Justin
thanks for your reply,
I did it. when I put the .n2t in my working directory,I have gotten this
error.
What error?
-Justin
--
==
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department o
Dear Justin
I want a topology for an arbitrary molecule (44 atom) and I use x2top
program that .n2t file is it’s input.
The .pdb file is as the following:
ATOM 1 O5 TPT 1 -6.131 -0.245 0.000 0.00
ATOM 2 C21 TPT 1 -5.041 0.384 0.000 0.00
ATOM
On 7/19/13 9:32 AM, afsaneh maleki wrote:
Dear Justin
I want a topology for an arbitrary molecule (44 atom) and I use x2top
program that .n2t file is it’s input.
The .pdb file is as the following:
ATOM 1 O5 TPT 1 -6.131 -0.245 0.000 0.00
ATOM 2 C21 TPT 1
Dear Justin
I copied all of files in oplsaa.ff folder in my working directory and
edited the atomname2type.n2t file as mentioned in before post in my working
directory.
I used these command:
] g_x2top –f .pdb –o .top -pbc –ff oplsaa
And gromacs get me:
opening force field file
/usr/
On 7/19/13 10:06 AM, afsaneh maleki wrote:
Dear Justin
I copied all of files in oplsaa.ff folder in my working directory and
edited the atomname2type.n2t file as mentioned in before post in my working
directory.
I used these command:
] g_x2top –f .pdb –o .top -pbc –ff oplsaa
And gr
Hi!
On 2013-07-17 21:08, Mark Abraham wrote:
You tried ppn3 (with and without --loadbalance)?
I was testing on 8-replicas simulation.
1) Without --loadbalance and -np 8.
Excerpts from the script:
#PBS -l nodes=8:ppn=3
setenv OMP_NUM_THREADS 4
mpiexec mdrun_mpi -v -cpt 20 -multi 8 -ntomp 4 -re
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