Dear all
I want to ask one basic question i.e is it possible to do
simulation of DNA model with gromacs ? If it possible which force field will
be suitable for this?
I am waiting for yours reply.
thanks a lot in advance.
Nitu sharma
Please, take a look at acpypi.googlecode.com. I hope it can help you.
Alan
On Wed, May 13, 2009 at 06:12, gmx-users-requ...@gromacs.org wrote:
Subject: [gmx-users] DNA-ligand interactions with AMBER
Dear Gromacs users
I am simulating the interactions between ligands and DNA
using GROMACS
Hello everyone,
I'm coming back to Gromacs. Before installing gromacs on our new SC I want to
do it on my desktop running SuSe 11.1 on an Intel Core2 Quad Q6700 @2.66GHz
CPU-arch.
Gromacs version 4.0.3
gmxtests version 4.0.4
1. Are these compatible? I could find neither a testset for 4.0.3
Dear all
I am getting problem in running pdb2gmx command on
DNA_protein file . The prblem is
Program pdb2gmx, VERSION 4.0.3
Source code file: resall.c, line: 426
Fatal error:
Residue 'T' not found in residue topology
Peyman Yamin wrote:
Hello everyone,
I'm coming back to Gromacs. Before installing gromacs on our new SC I want to
do it on my desktop running SuSe 11.1 on an Intel Core2 Quad Q6700 @2.66GHz
CPU-arch.
Gromacs version 4.0.3
gmxtests version 4.0.4
1. Are these compatible? I could find
nitu sharma wrote:
Dear all
I am getting problem in running pdb2gmx command on
DNA_protein file . The prblem is
Program pdb2gmx, VERSION 4.0.3
Source code file: resall.c, line: 426
Fatal error:
Residue 'T' not
Hey Mark,
thanks for the swift reply.
I installed 4.0.5 now. with the same testset it failes this time on some of
the kernel tests though all pdb2gmx ones pass.
As far as I understood, I should simply ignore it?
I didn't use --enable-mpi but when I run test script with -np 4, it does the
Peyman Yamin wrote:
Hey Mark,
thanks for the swift reply.
I installed 4.0.5 now. with the same testset it failes this time on some of
the kernel tests though all pdb2gmx ones pass.
As far as I understood, I should simply ignore it?
Probably. If there's a problem, it's probably not yours.
nitu sharma wrote:
Dear all
I want to ask one basic question i.e is it possible to
do simulation of DNA model with gromacs ? If it possible which force
field will be suitable for this?
Yes. Check out the force field .rtp files to see which contain parameters for
Dear sir/Madam Thanks in Advance
i am sorry for asking the same question again reg
MOPAC/gromacs installation. i did dos2linux coversion in two different online
sever but when i use output of one server i got the error as follows when i
type ./configure command
Dear sir/Madam Thanks in Advance
i am sorry for asking the same question again reg
MOPAC/gromacs installation. i did dos2linux coversion in two different online
sever but when i use output of one server i got the error as follows when i
type ./configure command
vidhya sankar wrote:
Dear sir/Madam Thanks in Advance
i am sorry for asking the same question
again reg MOPAC/gromacs installation. i did dos2linux coversion in two
different online sever but when i use output of one server i got the
error as follows when i type
Dear gmx users,
I run lipid bilayer simulations in parallel (gromacs v4.0.2), and I have fatal
error:
4 particles communicated to PME node 2 are more than a cell length out of the
domain
decomposition cell of their charge group
How can I fix it? Thank you in advance
Best regards,
Pavel I.
Pavel Semenyuk wrote:
Dear gmx users,
I run lipid bilayer simulations in parallel (gromacs v4.0.2), and I have fatal
error:
4 particles communicated to PME node 2 are more than a cell length out of the
domain
decomposition cell of their charge group
How can I fix it? Thank you in advance
I
Hello,
I would like to add non-polar hydrogens as well as the polar ones.
Does anybody know if that is possible?
I haven't found any related option of the function pdb2gmx.
Thanks,
Stefano.
___
gmx-users mailing listgmx-users@gromacs.org
Dear All,
I ran a POPC simuIation in gromacs 3.3.1 with the martini force field and it
ran fine. But I am getting the following error when I run it in gromacs
4.0.4. It seems there is some problem with the way the topology is built,
but I cannot find out what the problem is?
A list of missing
Stefano Meliga wrote:
Hello,
I would like to add non-polar hydrogens as well as the polar ones.
Does anybody know if that is possible?
I haven't found any related option of the function pdb2gmx.
protonate -h
-Justin
Thanks,
Stefano.
___
Don't know about the missing interactions ... never seen this in any
of the
gmx versions using Martini ...
for the error you should increase the -rdd to 1.4/1.5 nm
On May 13, 2009, at 4:36 PM, maria goranovic wrote:
Dear All,
I ran a POPC simuIation in gromacs 3.3.1 with the martini
Thank you very much!
Paulo Netz
On 5/13/09, Alan alanwil...@gmail.com wrote:
Please, take a look at acpypi.googlecode.com. I hope it can help you.
Alan
On Wed, May 13, 2009 at 06:12, gmx-users-requ...@gromacs.org wrote:
Subject: [gmx-users] DNA-ligand interactions with AMBER
Dear
I am doing some simulations involving high pressure condensation of
hydrocarbons. I have read that Gromacs can be used for condensation analysis.
I have been looking at the g_cluster and g_clustsize commands, and I think that
they will be my tools. My main question is that if I am using
Hi Users,
I constructed a .pdb file for TIP4P water model which I tried to convert to
.gro using pdb2gmx using:
$ pdb2gmx -f Sim1.pdb -o Sim1.gro -water tip4p
with the choice of forcefield as 5 (OPLS-AA/L all-atom force field). After
conversion I found that the position of HW3(MW), the dummy
Manik Mayur wrote:
Hi Users,
I constructed a .pdb file for TIP4P water model which I tried to convert
to .gro using pdb2gmx using:
$ pdb2gmx -f Sim1.pdb -o Sim1.gro -water tip4p
There is no need to use pdb2gmx.
If you just need a TIP4P solvent box, one exists in the /share/top
On Thu, May 14, 2009 at 1:32 AM, Justin A. Lemkul jalem...@vt.edu wrote:
Manik Mayur wrote:
Hi Users,
I constructed a .pdb file for TIP4P water model which I tried to convert
to .gro using pdb2gmx using:
$ pdb2gmx -f Sim1.pdb -o Sim1.gro -water tip4p
There is no need to use pdb2gmx.
Manik Mayur wrote:
On Thu, May 14, 2009 at 1:32 AM, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu wrote:
Manik Mayur wrote:
Hi Users,
I constructed a .pdb file for TIP4P water model which I tried to
convert to .gro using pdb2gmx using:
$
On Thu, May 14, 2009 at 1:56 AM, Justin A. Lemkul jalem...@vt.edu wrote:
Manik Mayur wrote:
On Thu, May 14, 2009 at 1:32 AM, Justin A. Lemkul jalem...@vt.edumailto:
jalem...@vt.edu wrote:
Manik Mayur wrote:
Hi Users,
I constructed a .pdb file for TIP4P water model
Hi Gmx,
I often hear the notion that simulations get stuck in local minima
(for potential energy I assume), how come? What happens to the
kinetic energy that is supposed to kick the system out of local
minima? (ie. when I roll a marble down a dip it tends to come out so
long as there's
Are there any good tutorials that start from the very beginning, like assuming
you only have a .pdb file? It seems that most of the tutorials I've found have
already generated the files you need and then all you have to do is punch in
some commands. Where can I learn to actually write the
There are many:
http://wiki.gromacs.org/index.php/Tutorials
-Justin
Joseph Johnson wrote:
Are there any good tutorials that start from the very beginning, like
assuming you only have a .pdb file? It seems that most of the tutorials
I've found have already generated the files you need and
http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_
residue_topology_database
Catch ya,
Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
The Gromacs tutorial is a good place for us who is stating. Another place is
the Gromacs wiki which has a beginner section (
http://wiki.gromacs.org/index.php/Beginners). In this local, it's possible
you to see some videos.
I suggest for you read the online manual where has the flow chart and get
Thanks for quick answer.
But I'd faced another problem. When I compile gromacs 4.0.5, it crash with
error Cannot
find fftw3f library, instead of my FFTW is in single precision, and I'd
exported to
CPPFLAGS and LDFLAGS real paths for libs. What is reason?
Thanks for help..
Best regards,
Pavel
Pavel Semenyuk wrote:
Thanks for quick answer.
But I'd faced another problem. When I compile gromacs 4.0.5, it crash with error
Cannot
find fftw3f library, instead of my FFTW is in single precision, and I'd
exported to
CPPFLAGS and LDFLAGS real paths for libs. What is reason?
Thanks for
yutong.z...@utoronto.ca wrote:
Hi Gmx,
I often hear the notion that simulations get stuck in local minima
(for potential energy I assume), how come? What happens to the kinetic
energy that is supposed to kick the system out of local minima? (ie.
when I roll a marble down a dip it tends to
Dear Mark
Thanks for your kind reply . Actually I am just starting the
simulation of DnA-protein complex using gromacs. I got the amber charged
force field ( to find DNA residues) from golovin_at_genebee.msu.su and
burnnick_u_at_rambler.ru this site . The name of force field is
Exact same question was answered just last month .
http://www.gromacs.org/pipermail/gmx-users/2009-April/040974.html
Catch ya,
Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC
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