Hi
I have been trying to run simulation on a cluster consisting of 24 nodes
Intel(R) Xeon(R) CPU X5670 @ 2.93GHz. Each node has 12 processors and they
are connected via 1Gbit Ethernet and Infiniband interconnect. The batch
system is TORQUE. However due to some issues with the parallel queue I
Dear Gromacs users
-- Iam trying to perform free energy calculation for
protein-ligand complex.
--Can any one plz suggess an appropriate tutorial to be
follow to perform this analysis
--
Thanks Regards
N.NagaSundaram
--
gmx-users mailing listgmx-users@gromacs.org
Thanks for the response. On further investigation, the problem only seems
to occur in jobs running via MPI on our GPU-enabled nodes, even if the
simulation in question doesn't use GPUs. Re-compiling gromacs 4.6.3 without
CUDA support eliminates the memory-hogging behavior. However, I'd like to
Actually,
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/
there are two different manuals - one about free energy calculation and
other about protein ligand complexes.
This page is also can be helpfull
http://www.alchemistry.org/wiki/Category:Free_Energy_How-to%27s
Actually,
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/
there are two different manuals - one about free energy calculation and
other about protein ligand complexes.
This page is also can be helpfull
http://www.alchemistry.org/wiki/Category:Free_Energy_How-to%27s
Hi,
make a scaling test and run on a single node only at first. So you can
estimate what performance you can at most expect when going to more nodes.
On a single node, you can also run with Gromacs' thread-MPI, thus
eliminating the possibility that something with your MPI is wrong.
There are
Dear all,
I am developing the force field paramters of an organic molecule. I have a
trouble when i wrote the hydrogen atom database (.hdb) file. I do not know how
to write to control atom. The manual said that:
Three or four control atoms (i,j,k,l), where the first always is the atom to
Indeed - your question was fair, and no undue criticism pertained! :-)
If you are trying to reproduce something, you must expect .tpr
differences between 4.0.x and 4.6.y. I illustrated the change that has
taken place in how VDW parameters are used internally in 4.6, and how
that is distinct from
On 9/19/13 12:33 AM, Zhikun wrote:
Dear users,
Recently I have been trying to use xdrfile libray to read trajectory
.trr file in my own C++ code. Now I can just read the coordinates of all
atoms at each time frame. But I don't know how to select certain types of
atoms from the trajectory
On 9/19/13 5:40 AM, xiao wrote:
Dear all,
I am developing the force field paramters of an organic molecule. I have a
trouble when i wrote the hydrogen atom database (.hdb) file. I do not know how
to write to control atom. The manual said that:
Three or four control atoms (i,j,k,l), where
There are some starter files here:
http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_free_energy_calculations%3a_Michael_Shirts%2c_Session_2A
Which can be used in conjunction with the Alchemistry.org instructions.
But it needs to be
Dear all,
I am learning the parallelization issues from the instructions on Gromacs
website. I guess I got a rough understanding of MPI, thread-MPI, OpenMP. But I
hope to get some advice about a correct way to run jobs.
Say I have a local desktop having 16 cores. If I just want to run jobs on
Thank you Carsten
Will surely try out the suggestions and get back to you
On Thu, Sep 19, 2013 at 1:52 PM, Carsten Kutzner ckut...@gwdg.de wrote:
Hi,
make a scaling test and run on a single node only at first. So you can
estimate what performance you can at most expect when going to more
On 9/19/13 10:12 AM, fatemeh ramezani wrote:
dear users
I'm studying gold nano-particle effect on one of the blood protein stability
and structure. one time I simulated the protein in the presence of the gold
nanoparticle and once without nanoparticles.
when I simulated protein alone in
On 9/19/13 10:38 AM, Ray Sheppard wrote:
Hello,
On the page sited above, it says:
General GROMACS Use
* A step-by-step demo and several simple examples are available in the
share/tutor subdirectory of your GROMACS installation.
However, In the tarfile for version 4.6.3, the
Hello,
On the page sited above, it says:
General GROMACS Use
* A step-by-step demo and several simple examples are available in the
share/tutor subdirectory of your GROMACS installation.
However, In the tarfile for version 4.6.3, the directories under share
are:
Thanks, Mark.
Just compiled gmx 4.0.5 and created tpr with the 'published' topology file.
Ver. 4.0.5 seems to be the version that was used to create the 'published'
tpr file. The only differences now that matter are these c6 and c12 terms.
Is there any mdp options that may change how c6 and c12
dear users
I'm studying gold nano-particle effect on one of the blood protein stability
and structure. one time I simulated the protein in the presence of the gold
nanoparticle and once without nanoparticles.
when I simulated protein alone in water, I expected the protein to remain
stable
Hi Shahab,
You edited the .gro file, but you made an error. So you have to read the
manual to understand the file format and then see where and how your edited
file doesn't match.
Cheers,
Tsjerk
On Thu, Sep 19, 2013 at 5:00 PM, shahab shariati
shahab.shari...@gmail.comwrote:
Dear Tsjerk
Dear Tsjerk
Thanks for your consideration.
I ignored Warning 1.
WARNING 1 [file topol.top, line 32]:
3632 non-matching atom names
atom names from topol.top will be used
atom names from system.gro will be ignored
Based on your suggestion, I checked non-matching
atom names between
Dear Sir,
The tool gmx gangle is wonderful. The additional options are very
flexible and easy to use.
@Teemu Murtola: Are there any modifications to the other gmx tools? (eg:
rdf calculation with dynamic selection...etc). I am trying to explore the
new version.
Thank you
On Tue, Sep 17, 2013 at
On 9/19/13 11:59 AM, fatemeh ramezani wrote:
Dear Justin
I used gromacs OPLSAA forcefield for simulation of protein and TIP3P model for
water.
em.mdp file:
title = n.pdb
cpp = /lib/cpp
define = -DFLEXIBLE
constraints = none
Hey All,
I am running a simulation of a POPC bilayer in water using a Charmm 36
forcefield. I am having trouble using cutoff-scheme=Verlet in my nvt
equilibration.
My .mdp file is as follows:
title= OPLS Lysozyme NVT equilibration
define = -DPOSRES ; position restrain the protein
Dear Justin
I used gromacs OPLSAA forcefield for simulation of protein and TIP3P model for
water.
em.mdp file:
title = n.pdb
cpp = /lib/cpp
define = -DFLEXIBLE
constraints = none
integrator = steep
nsteps = 4
Hi,
I am trying to perform SDFs using g_spatial tool from Gromacs.
I did all steps, recommended and indicated in Gromacs' manual,
1. Use make_ndx to create a group containing the atoms around which you want
the SDF
2. trjconv -s a.tpr -f a.xtc -o b.xtc -center tric -ur compact -pbc none
3.
On 9/19/13 2:21 PM, akk5r wrote:
Hey All,
I am running a simulation of a POPC bilayer in water using a Charmm 36
forcefield. I am having trouble using cutoff-scheme=Verlet in my nvt
equilibration.
My .mdp file is as follows:
title= OPLS Lysozyme NVT equilibration
define = -DPOSRES
On 9/19/13 2:56 PM, Marta Batista wrote:
Hi,
I am trying to perform SDFs using g_spatial tool from Gromacs.
I did all steps, recommended and indicated in Gromacs' manual,
1. Use make_ndx to create a group containing the atoms around which you want
the SDF
2. trjconv -s a.tpr -f a.xtc -o
Hmm, I will have to do some more controls then, but I prob dont have time
to do them till after quals this fall...
You mention Hartree-Fock methods, does this mean that you disfavor DFT for
some reason for this purpose?
On Tue, Sep 17, 2013 at 5:40 PM, Justin Lemkul jalem...@vt.edu wrote:
Sulpher is important, but it is in the apoprotein, not the parametrized
prosthetic group
On Thu, Sep 19, 2013 at 6:51 PM, Rafael I. Silverman y de la Vega
rsilv...@ucsc.edu wrote:
Hmm, I will have to do some more controls then, but I prob dont have time
to do them till after quals this
Thanks Justin. I was told that the vdwtype = switch was an essential
component of running Charmm36. Is that not the case?
--
View this message in context:
http://gromacs.5086.x6.nabble.com/Charmm-36-forcefield-with-verlet-cut-off-scheme-tp5011322p5011328.html
Sent from the GROMACS Users Forum
On 9/19/13 9:51 PM, Rafael I. Silverman y de la Vega wrote:
Sulpher is important, but it is in the apoprotein, not the parametrized
prosthetic group
I only mentioned this as one example where user input and intuition is useful,
not necessarily to directly comment on anything you are doing.
On 9/19/13 9:51 PM, Rafael I. Silverman y de la Vega wrote:
Hmm, I will have to do some more controls then, but I prob dont have time
to do them till after quals this fall...
You mention Hartree-Fock methods, does this mean that you disfavor DFT for
some reason for this purpose?
For
On 9/19/13 9:55 PM, akk5r wrote:
Thanks Justin. I was told that the vdwtype = switch was an essential
component of running Charmm36. Is that not the case?
It is, but I suppose one can achieve a similar effect with the Verlet scheme.
You can certainly use the traditional CHARMM settings if
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