Hello to everybody,
I am new in atomistic simulations and a have some doubts about how to do it.
I wanna simulate a mixture of Cyclohexane, Toluene and Dodecane.
My questions are, ¿Where do I get the pdb files of these molecules
from? and ¿How do I know which force field I should choose in
Dear Gromacs users,
I am using Gromacs in a computer cluster using many processors (currently
228). Sometimes I get the following assertion error:
*Assertion `timerq-cursor = current_time' failed at mxm/util/timerq.c:91*
This error presents at some time inside of the simulation, every run at a
I've just started doing atomistic simulations over the last few weeks as well
and can share what I've learned so far.
I have been using 'automated topology builder'. It only uses the gromos 53a6
forcefield so eliminates the choice if you want to use it. ATB generates the
pdb and itp files for
On 12/3/13 6:17 AM, Hardy, Adam wrote:
I've just started doing atomistic simulations over the last few weeks as well
and can share what I've learned so far.
I have been using 'automated topology builder'. It only uses the gromos 53a6
forcefield so eliminates the choice if you want to use
It is an interesting question, because how does one generate velocities at
0 K?
Random sampling from a Maxwellian distribution with mean zero and zero
width :) At the end of the first step all velocities will be scaled to
zero. That shouldn't be very unstable.
Cheers,
Tsjerk
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Gromacs
Dear Users,
I am using a cluster of 64 cores to perform my MD simulations using GROMACS
version 4.5.5.
I would be glad to know the exact mdrun command that will allow me use the
available resources.
Thank you.
*Do all the good you can, By all the means you can, In all the ways you
can,
On 12/3/13 10:23 AM, MUSYOKA THOMMAS wrote:
Dear Users,
I am using a cluster of 64 cores to perform my MD simulations using GROMACS
version 4.5.5.
I would be glad to know the exact mdrun command that will allow me use the
available resources.
The answer depends entirely on the
Dear Justin,
Well it seems i am the first one to do MD simulations in my lab and i am
using a chemistry department cluster and nobody has prior knowledge on
GROMACS. I can use all the cores in the cluster but need to know if there
is a specific mdrun command that can allow me specify the number of
I am having difficulty running a simulation with virtual particles. If I use
the group cutoff-scheme, the simulation runs, but if I use Verlet cutoff, i
get the error The mass of a vsiten constructing atom is = 0.
Does Verlet cutoff scheme not work with virtual particles, or is there some
trick
Hello Everyone,
ambconv.tgz (
http://www.gromacs.org/Downloads/User_contributions/Other_software) tool
exists for converting Amer input files into the ones for Gromacs. Now, it's
README-eng file says that two Amber input files ( .atop (topology) and
.rst (coordinates) ) are needed to generate
On 12/03/2013 11:45 AM, Chetan Mahajan wrote:
are there other tools to convert Amber input files
into the ones for Gromacs?
I've had success with acpype:
https://code.google.com/p/acpype/
Use the amb2gmx mode:
acpype -p _prmtop_ -x _inpcrd_
--
Wes Barnett | jbarn...@tulane.edu
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Gromacs
Dear Users
I have a problem about production step in MD simulation. Can this step be run
with constraints or unconstraints?
Best Regards
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Hi,
I haven't tried it but it should work if you set verlet-buffer-drift=-1 and
set rlist manually.
Roland
On Mon, Dec 2, 2013 at 3:20 PM, Brad Van Oosten bv0...@brocku.ca wrote:
I am trying to add virtual sites to a simulation with no mass or charge,
just
to make tracking the center of
The invocation line depends on the MPI tool installed on the cluster.
E.g. in case of openmpi, you write
openmpi -np 64 mdrun -dd 4 4 4
Dr. Vitaly V. Chaban
On Tue, Dec 3, 2013 at 4:58 PM, MUSYOKA THOMMAS
mutemibiochemis...@gmail.com wrote:
Dear Justin,
Well it seems i am the first one to
Dear Users,
does anyone know what was the resolution of this bug?
http://redmine.gromacs.org/issues/554
How does one handle pdb2gmx with PDB files and avoid errors like this?
Atom HB3 in residue ASP 2 was not found in rtp entry ASP with 14 atoms
while sorting atoms.
Thanks
Mikhail
THis looks interesting, However, any version is giving following error on
test mentioned in README:
../acpype.py -i FFF.pdb
File ../acpype.py, line 1231
with open(pklFile, wb) as f: # for python 2.6 or higher
^
SyntaxError: invalid syntax
Unfortunately, I do not know python.
THis looks interesting, However, any version is giving following error on
test mentioned in README:
../acpype.py -i FFF.pdb
File ../acpype.py, line 1231
with open(pklFile, wb) as f: # for python 2.6 or higher
^
SyntaxError: invalid syntax
Unfortunately, I do not know python.
You shouldn't change any of the code unless you know what you're doing. If you
remove lines it will not work as intended.
I think you simply need to upgrade your version of Python 2, according to the
error message.
jbarn...@tulane.edu | from mobile
Chetan Mahajan chetanv...@gmail.com wrote:
Thanks, James. I already have python 2.4.
regards
Chetan
On Tue, Dec 3, 2013 at 8:45 PM, Barnett, James W. jbarn...@tulane.eduwrote:
You shouldn't change any of the code unless you know what you're doing. If
you remove lines it will not work as intended.
I think you simply need to upgrade
hi chandan..
output for ls -1 is as follows:
the directory from where i am running simulatons is in desktop .. and i have
all the permissions for it. i am not that used to ubuntu and your suggestion
will be of great help ..
total 52
drwxrwxrwx 9 vansh vansh 4096 Nov 22 14:40 Desktop
drwxr-xr-x 2
Sir,
I want to do an REMD simulation having 16 replicas. But I have only
8 processors. Is it possible to do 16 replicas in 8 processors? How I can
do this?
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Dear vaani,
Please rerun the gmx executable.
Chandan
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Chandan kumar Choudhury
NCL, Pune
INDIA
On Wed, Dec 4, 2013 at 11:20 AM, vaani vsha...@imtech.res.in wrote:
hi chandan..
output for ls -1 is as follows:
the directory from where i am running simulatons is in desktop .. and i
have
Dear vaani,
Sorry for the unclear message. Try running the mdrun command once again and
post the out put of the log file.
Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Wed, Dec 4, 2013 at 12:34 PM, vaani vsha...@imtech.res.in wrote:
i am sorry ..but i kind of dint get you ..
-
sure ..
-
thanks in advance :)
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View this message in context:
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Below information might be of interest to the Gromacs
development/optimization team.
What can we derive from the 10% md_run speedup when PCIE3.0 speed increases
from 5GT/s-8GT/s?
A 60% PCIE speed increase results in a 10% run time reduction.
Hence about 10/60=17% of the run time gets spent in
vaani wrote nvt.log
http://gromacs.5086.x6.nabble.com/file/n5013030/nvt.log
find the attached nvt.log file ..
i have been equilibrating for 200ps in this example..and getting this error
,
but when equilibrating for 100ps there is no such error ..in later case i am
getting this error at the
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