Hey Lin,
Did you consider PBC?
Also, I wouldn't include the bromide if I were you, as it just adds noise,
because it can move around freely. You seem to be interested in the change
in dipole moment in the cation only, anyway.
Cheers,
Tsjerk
On Oct 21, 2010 7:02 AM, Chih-Ying Lin
Hi justin
I found what went wrong and i corrected my mdp file.now the system
equilibrated to the desired temperature 300 K (plus r minus 30 K) is this
ok?
Apart from that i want to know how you plot the average running pressure and
density in your tutorial for lyzosyme (redline). i just want to
Dear Justin
If I do two MD simulations for a short time in the same conditions(of
course separately for protein and drug)
and calculate total energy of each one and sum them with each other as E1
as nonbonding free energy of system.
then a MD simulation for Protein-drug system in the same
Hi Mohsen,
The mean energy difference is only one component of the free energy difference.
Before you go any further I'd suggest reading a good book on molecular
simulations, like 'Understanding Molecular Simulations' by Frenkel and Smit.
There's a good reason free energy calculations cover
reconsider your statement about the displacement vector. You should try
to understand the concepts of vectors and reference points first. It is
absolutely mandatory to do so before calculating dipole moments of
charged systems. It might also be wise to use a small test system to
practice on.
Actually, I believe that using the energy difference, Delta E, as an
approximation to the free energy difference, Delta G, is a valid
approach (which I'm considering myself). The entropic contribution to
Delta G, namely -T Delta S, may be less prominent than Delta E.
In addition, Delta S can be
On 2010-10-21 10.39, Ehud Schreiber wrote:
Actually, I believe that using the energy difference, Delta E, as an
approximation to the free energy difference, Delta G, is a valid
approach (which I'm considering myself). The entropic contribution to
Delta G, namely -T Delta S, may be less prominent
Hi,
does anyone have experience with AMD's 12-core Magny-Cours
processors? With 48 cores on a node it is essential that the processes
are properly pinned to the cores for optimum performance. Numactl
can do this, but at the moment I do not get good performance with
4.5.1 and threads, which still
Hi,
We haven't observed any problems running with threads over 24 core AMD nodes
(4x6 cores).
Berk
From: ckut...@gwdg.de
Date: Thu, 21 Oct 2010 12:03:00 +0200
To: gmx-users@gromacs.org
Subject: [gmx-users] Gromacs 4.5.1 on 48 core magny-cours AMDs
Hi,
does anyone have experience
Hi Carsten,
As Berk noted, we haven't had problems on 24-core machines, but quite frankly I
haven't looked at thread migration.
Currently, the wait states actively yield to the scheduler, which is an
opportunity for the scheduler to re-assign threads to different cores. I could
set harder
Dear Gromacs users,
I am new user Gromacs. I want to study on protein simulation using gromacs.
If possible, Can you send a few articles on the protein simulation using
Gromacs?For example, I downloaded from Protein Data Base the PDB extension
file of any protein. What is the purpose of protein
Karel Berka wrote:
Hi all,
I have detected that preference in reading forcefield files in Gromacs
4.5 has probably been changed from Gromacs 4.0.x and older.
In older gromacs, when there was forcefield with modification present in
my working directory, then it was read
vinothkumar mohanakrishnan wrote:
Hi justin
I found what went wrong and i corrected my mdp file.now the system
equilibrated to the desired temperature 300 K (plus r minus 30 K) is
this ok?
This is impossible to assess without seeing your .mdp settings. A fluctuation
of 10% is probably
Ahmet,
For starting you can read Leach's book (Molecular modeling: principles and
applications). This book gives you theoretical background and opinion about
application areas of molecular dynamics (MD) simulation. Gromacs is only a
simulation tool to do MD simulation, after understanding MD you
Karel Berka wrote:
Karel Berka wrote:
Hi all,
I have detected that preference in reading forcefield files in
Gromacs
4.5 has probably been changed from Gromacs 4.0.x and older.
In older gromacs, when there was forcefield with modification
present in
Hi,
use ISI Web of Knowledge or scholar.google, search for 'protein +
gromacs' and you should get tons of results.
Greetings
Thomas
Date: Thu, 21 Oct 2010 13:29:11 +0300
From: ahmet y?ld?r?mahmedo...@gmail.com
Subject: [gmx-users] published paper related to protein simulation
using
Hi,
I think, started from some gromacs tutorial is a nice ideas and then during
those process you certainly will meet some paper.
lina
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Thomas Schlesier
Hi Justin
Below is my nvt.mdp (nvt equilibration) file.i think probably you can have
look at it and its not such big.
define = -DFLEXIBLE
integrator = md
nsteps = 5
dt= 0.002
nstxout
vinothkumar mohanakrishnan wrote:
Hi Justin
Below is my nvt.mdp (nvt equilibration) file.i think probably you can
have look at it and its not such big.
define = -DFLEXIBLE
You should never run MD with flexible water. All the water models included in
Gromacs
Hi Sander,
On Oct 21, 2010, at 12:27 PM, Sander Pronk wrote:
Hi Carsten,
As Berk noted, we haven't had problems on 24-core machines, but quite frankly
I haven't looked at thread migration.
I did not have any problems on 32-core machines as well, only on 48-core ones.
Currently, the
vinothkumar mohanakrishnan wrote:
Hi Justin
Thank you for your suggestion. I am doing equilibration of DCE (108
molecules) alone in a box and there is no water molecule inside the box.
cant i use -DFLEXIBLE for DCE?. by the way i will try your suggestion
about xmgrace.
In that case,
Dear gmx-users,
recently Pär Bjelkmar and Thomas Piggot have generated force field files
for Charmm36 lipids. I run some simulations to find the best run
parameters and to check if the results of the original Charmm36 lipid
article [Klauda et al., J. Phys Chem. B, 2010, 114, 7830) can be
Hi,
You have very strange and complex cut-off settings in Gromacs.
What Charmm settings are you trying to mimic?
Berk
Date: Thu, 21 Oct 2010 15:03:51 +0200
From: jakobtorwei...@tuhh.de
To: gmx-users@gromacs.org
Subject: [gmx-users] CHARMM36 lipid bilayers
Dear gmx-users,
recently Pär
Hello,
I am working on a system which has a diatomic solute surrounded by water
molecules.
I want to calculate the energy for each step with and with out charge on
solute simultaneously.
Pl. help me solve this problem.
Nilesh
--
gmx-users mailing listgmx-users@gromacs.org
On 21/10/2010 11:55 PM, Nilesh Dhumal wrote:
Hello,
I am working on a system which has a diatomic solute surrounded by water
molecules.
I want to calculate the energy for each step with and with out charge on
solute simultaneously.
Pl. help me solve this problem.
I don't understand what you
I am doing solvation dynamics for my system.
I have system with diatomic (PA---NE)solute surrounded by water molecules.
I want to run simulation with two differcent cases.
1. PA charge=0 and NE charge=0 : No charge on solute
2. PA charge=+1 and NE charge=-1 : Charge on solute
I want to calculate
Nilesh Dhumal wrote:
I am doing solvation dynamics for my system.
I have system with diatomic (PA---NE)solute surrounded by water molecules.
I want to run simulation with two differcent cases.
1. PA charge=0 and NE charge=0 : No charge on solute
2. PA charge=+1 and NE charge=-1 : Charge on
On 22/10/2010 1:17 AM, Nilesh Dhumal wrote:
I am doing solvation dynamics for my system.
I have system with diatomic (PA---NE)solute surrounded by water molecules.
I want to run simulation with two differcent cases.
1. PA charge=0 and NE charge=0 : No charge on solute
2. PA charge=+1 and NE
Thanks for the information; the OpenMPI recommendation is probably because
OpenMPI goes to great lengths trying to avoid process migration. The numactl
doesn't prevent migration as far as I can tell: it controls where memory gets
allocated if it's NUMA.
For gromacs the setting should of
On Oct 21, 2010, at 4:44 PM, Sander Pronk wrote:
Thanks for the information; the OpenMPI recommendation is probably because
OpenMPI goes to great lengths trying to avoid process migration. The numactl
doesn't prevent migration as far as I can tell: it controls where memory gets
allocated
On 21 Oct 2010, at 16:50 , Carsten Kutzner wrote:
On Oct 21, 2010, at 4:44 PM, Sander Pronk wrote:
Thanks for the information; the OpenMPI recommendation is probably because
OpenMPI goes to great lengths trying to avoid process migration. The numactl
doesn't prevent migration as far as
Thanks for the information; the OpenMPI recommendation is probably because
OpenMPI goes to great lengths trying to avoid process migration. The
numactl doesn't prevent migration as far as I can tell: it controls where
memory gets allocated if it's NUMA.
My understanding is that processes
Hi Sven,
I have also seen similar things from the area per lipid of the bilayers
I have run (POPC and DPPC). I would suggest you try running with the
CHARMM TIP3P water (tips3p.itp) and see if you get values which are
closer to the ones published in the paper you mention. This will be
discussed
Hi,
FWIW, I have recently asked about this in the hwloc mailing list:
http://www.open-mpi.org/community/lists/hwloc-users/2010/10/0232.php
In general, hwloc is a useful tool for these things.
http://www.open-mpi.org/projects/hwloc/
Best,
Ondrej
On Thu, Oct 21, 2010 at 12:03, Carsten Kutzner
HI
dipole moment = 48.0 sum of q_i x_i
x_i is the atomic position.
The PBC is considered.
I did not include the counter ion of the salt molecule in my calculation.
The salt molecule is A-N(CH3)3-Br and it has two structures, cis and trans.
Here A are a string of atoms, most of them are carbons.
Dear All,
I am trying to equilibrate in NVT ensemble of a peptide with glycolipid (GL)
molecules in a cubic box filled with TIP3P water (from Mackerell et al.).
The force field for GL were converted to GROMACS format from CHARMM27 force
field with additional parameters non present in the
Hi
In one paper, the salt-molecule has two structures, trans and cis.
The sentence in the paper is that trans-structure is more hydrophobic than
the cis-structure without providing the value of the dipole moment.
I wonder know if the value of dipole moment is the main indicator to decide
if
HI
As Timo M.D. Graen described
As long as the system is neutral, the reference point will not affect the
calculation result of the dipole moment for the system.
On the other hand, I also play around the small salt-molecule as Timo M.D.
Graen suggested.
take two ions for a start, Na+ and Cl-,
On Thu, Oct 21, 2010 at 3:18 PM, Renato Freitas renato...@gmail.com wrote:
Hi gromacs users,
I have installed the lastest version of gromacs (4.5.1) in an i7 980X
(6 cores or 12 with HT on; 3.3 GHz) with 12GB of RAM and compiled its
mpi version. Also I compiled the GPU-accelerated
version
jagannath mondal wrote:
Hi,
I have used gromacs 4.0.7 to do MD simulation of two solutes A B
in water ( solvent) .
Initially, I had set energy groups = system and used mdrun to do the
simulation.
Now,I wanted to get the potential energy contribution from due to
interaction of A-A,
Justin,Thanks for your reply. Then I wonder whether there is any other way
out in gromacs to get the net interaction potential energy due to each of the
components in a simulations.
I am asking this, many times people report the potential energy contribution
due to solvent-solvent
jagannath mondal wrote:
Justin,
Thanks for your reply. Then I wonder whether there is any other way
out in gromacs to get the net interaction potential energy due to each
of the components in a simulations.
I am asking this, many times people report the potential energy
contribution due
Thanks Roland. I will do a newer test using the fourier spacing equal
to 0.11. However, about the performance of GPU versus CPU (mpi) let me
try to explain it better:
The simulation using gromacs with GPU started and finished:
Started mdrun on node 0 Wed Oct 20 09:52:09 2010
Finished mdrun on
Hi, I was wondering whether gromacs can calculate a quantity called molecular
surface area(MSA) which is different from solvent accessible surface area(SASA).
By definition, SASA of a molecule is the area of surface traced by center of a
spherical water probe rolling on a vander wall surface of
What you want then is a Connolly surface?
Which I gather is what GROMACS actually calculates,
http://www.mail-archive.com/gmx-users@gromacs.org/msg12518.html
Catch ya,
Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
On Thu, Oct 21, 2010 at 5:53 PM, Renato Freitas renato...@gmail.com wrote:
Thanks Roland. I will do a newer test using the fourier spacing equal
to 0.11.
I'd also suggest to look at g_tune_pme and run with different rcoulomb,
fourier_spacing. As long as the ratio is the same you get the same
Hi
When I issued the command g_dipole,
the dialog poped out and asked me to select a group.
1. system
2. protein
.
11. solvent
12. the rest of the salt-molecule except its counter ion
13. counter ions (CL-)
If I select #12, Gromacs will not consider counter ions to calculate the
On 22/10/2010 8:21 AM, jagannath mondal wrote:
Hi,
I have used gromacs 4.0.7 to do MD simulation of two solutes A B
in water ( solvent) .
Initially, I had set energy groups = system and used mdrun to do
the simulation.
Now,I wanted to get the potential energy contribution from due to
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