Dear GMxers,
I want to simulate the proton transfer reaction in bulk water using
gromacs.I am not aware how to add proton using genion.Is it possible to add
excess protons like other ions.I could not find proton in ions.itp.
If anybody can guide me about the same.
Thanks
DeepaK Ojha
School Of
Hi DeepaK,
You should be aware that excess protons are not floating around freely
among a bunch of H2O. Whatever reasoning along this line is physically
meaningless (including thinking of a mixture of H3O+, H2O, OH-). This is
the realm of QM.
Cheers,
Tsjerk
On Thu, Oct 10, 2013 at 8:05 AM,
Hello,
Does anyone have experience running gromacs and data analysis tools on Stampede
or similar supercomputer. Do we have a set of best practices or approaches for
this situation.
Any input is highly appreciated.
Thanks
--
gmx-users mailing listgmx-users@gromacs.org
Dear Gromacs users,
I have asked this questions before and Justin gave some answers which I could
solve my problem based on his answer. I am using Ubuntu 12.10 and installed
gromacs 4.5.5-2.
this is what I have done
2- I moved this file to usr/local/bin
1- first I downloaded the dssp
wget
Hi,
Since the release of 4.5.5, DSSP totally changed its command-line
interface. So old GROMACS code cannot work with new DSSP. You need to get
the old version of DSSP to use with old GROMACS, or new GROMACS code to
work with either DSSP.
Mark
On Thu, Oct 10, 2013 at 1:37 PM, Mass
Dear Mark,
Thanks again for your response.
Many of the regression tests seem to have passed:
All 16 simple tests PASSED
All 19 complex tests PASSED
All 142 kernel tests PASSED
All 9 freeenergy tests PASSED
All 0 extra tests PASSED
Error not all 42 pdb2gmx tests have been done successfully
Only
Hi GMX users:
I am not sure when I prepared a itp file for molecule containing three virtual
site by manual.
there is two questions list below:
1) whether it is validate when I set up bonded interaction(bond,angle or
dihedral) between normal atom and virtual site ?
2) Is there any definition
How about applying position restarints with a strong force constant? What
is less computationally expensive: position restrained, freezing the whole
molecule? The nanotube should be rigid... Shall I place the edged of the
tube on the box edge as well and use pbc=xyz and periodic molecules = yes?
On 10/10/13 9:21 AM, Steven Neumann wrote:
How about applying position restarints with a strong force constant? What
is less computationally expensive: position restrained, freezing the whole
molecule? The nanotube should be rigid... Shall I place the edged of the
You shouldn't see any real
Thanks a lot. You the bond as a distance between atoms? I wish to avoid
bonds as they are not necessary...just position restraint. What would be
the force constant? I tried 1000 once without bonds and my atoms were
moving a bit...
Steven
On Thu, Oct 10, 2013 at 2:28 PM, Justin Lemkul
On 10/10/13 9:34 AM, Steven Neumann wrote:
Thanks a lot. You the bond as a distance between atoms? I wish to avoid
bonds as they are not necessary...just position restraint. What would be
the force constant? I tried 1000 once without bonds and my atoms were
moving a bit...
If you don't have
And also ... my tube has 1200 atoms and I wish to apply [ exclusions ] - is
there any gmx tool to exclude interactions within the given molecule so 1
with all 1200, 2 with all 1200...etc... 1200 with all 1200?
Steven
On Thu, Oct 10, 2013 at 2:34 PM, Steven Neumann s.neuman...@gmail.comwrote:
Thanks. I will place them then within the distance from the box edge =
distance between atoms within the tube right? I can create bonds and use
harmonic spring constant like for backbone protein atoms...but whats the
point when they do not move anyway? I am using NVT.
Steven
On Thu, Oct 10,
On 10/10/13 9:39 AM, Steven Neumann wrote:
And also ... my tube has 1200 atoms and I wish to apply [ exclusions ] - is
there any gmx tool to exclude interactions within the given molecule so 1
with all 1200, 2 with all 1200...etc... 1200 with all 1200?
No, but it's a simple script to write
On 10/10/13 9:44 AM, Steven Neumann wrote:
Thanks. I will place them then within the distance from the box edge =
distance between atoms within the tube right? I can create bonds and use
harmonic spring constant like for backbone protein atoms...but whats the
point when they do not move
Thank you. Would both be equal in terms of gaining computational time?
Steven
On Thu, Oct 10, 2013 at 2:46 PM, Justin Lemkul jalem...@vt.edu wrote:
On 10/10/13 9:39 AM, Steven Neumann wrote:
And also ... my tube has 1200 atoms and I wish to apply [ exclusions ] -
is
there any gmx tool
Thank you. I do not have any explicit solvent in my system. I included the
solvent in nonbonded parameters so not even implicit.
Steven
On Thu, Oct 10, 2013 at 2:47 PM, Justin Lemkul jalem...@vt.edu wrote:
On 10/10/13 9:44 AM, Steven Neumann wrote:
Thanks. I will place them then within
On 10/10/13 9:53 AM, Steven Neumann wrote:
Thank you. Would both be equal in terms of gaining computational time?
No idea. You definitely would not gain anything from using the [nonbond_params]
approach. Maybe with exclusions.
-Justin
--
On 10/10/13 9:54 AM, Steven Neumann wrote:
Thank you. I do not have any explicit solvent in my system. I included the
solvent in nonbonded parameters so not even implicit.
Well, presumably you have other things in the system, otherwise you're
simulating an inert tube of non-interacting
Thanks a lot. I will use position restraints then with a strong force
constant, no bonds and place the edge atoms within half of distance between
them from the box edge. Is that correct?
Steven
On Thu, Oct 10, 2013 at 2:56 PM, Justin Lemkul jalem...@vt.edu wrote:
On 10/10/13 9:54 AM, Steven
On 10/10/13 10:01 AM, Steven Neumann wrote:
Thanks a lot. I will use position restraints then with a strong force
constant, no bonds and place the edge atoms within half of distance between
them from the box edge. Is that correct?
Seems reasonable. One way to find out...
-Justin
--
Hi,
GROMACS does not have Xeon Phi support, so you'll be better off using
only the CPUs in Stampede. Porting and optimization is in progress,
but it will probably be a few months before you can test some
Phi-optimized mdrun.
Running (most) analyses on Phi is not really feasible. While there are
Thank you!
Steven
On Thu, Oct 10, 2013 at 3:02 PM, Justin Lemkul jalem...@vt.edu wrote:
On 10/10/13 10:01 AM, Steven Neumann wrote:
Thanks a lot. I will use position restraints then with a strong force
constant, no bonds and place the edge atoms within half of distance
between
them
DearAll,
when I am running NVT equilibration phase i am getting following error
Back Off! I just backed up step0c.pdb to ./#step0c.pdb.4#
Wrote pdb files with previous and current coordinates
starting mdrun 'Gromacs Runs On Most of All Computer Systems in water'
25 steps,500.0 ps.
On 10/10/13 10:21 AM, Nikhil Agrawal wrote:
DearAll,
when I am running NVT equilibration phase i am getting following error
Back Off! I just backed up step0c.pdb to ./#step0c.pdb.4#
Wrote pdb files with previous and current coordinates
starting mdrun 'Gromacs Runs On Most of All Computer
Hi, I'm new to both Gromacs and OPLS. I have always used CHARMM or AMBER
before so am a bit confused about some idiosyncrasies.
When I go to a production run on my system (a protein in a truncated octahedron
box of Tip4 water) I have removed all constraints. When I run grompp, I get an
On 10/10/13 12:17 PM, Martin, Erik W wrote:
Hi, I'm new to both Gromacs and OPLS. I have always used CHARMM or AMBER
before so am a bit confused about some idiosyncrasies.
When I go to a production run on my system (a protein in a truncated
octahedron box of Tip4 water) I have removed all
Taking a shot in the dark, when it happens immediately like that (step0) in
my experience it often means the topology is wrong.
On 10 Oct 2013 16:27, Justin Lemkul jalem...@vt.edu wrote:
On 10/10/13 10:21 AM, Nikhil Agrawal wrote:
DearAll,
when I am running NVT equilibration phase i am
OPLS-AA was generally derived with Monte Carlo, which means that all
bonds were exactly constrained. But read the papers!
On Thu, Oct 10, 2013 at 12:27 PM, Justin Lemkul jalem...@vt.edu wrote:
On 10/10/13 12:17 PM, Martin, Erik W wrote:
Hi, I'm new to both Gromacs and OPLS. I have always
Dear Arun:
here is how I compile fftw and gromacs on stampede.
I have also included a job script and a script to submit a chain of jobs.
As Szilárd notes, this does not use the MICs, but it is still a rather fast
machine.
# Compilation for single precision gromacs plus mdrun_mpi
#
Dear Mark,
Thanks for your comments, I uninstalled my previous Gromacs version ( from
Ubuntu software centre I just removed it) . and followed the dirty and quick
installation on Gromacs website
tar xfz gromacs-4.6.3.tar.gz
cd gromacs-4.6.3
mkdir build
cd build
cmake .. -DGMX_BUILD_OWN_FFTW=ON
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