It sounds like there is something wrong with the 'B' topology. Have you tried
the 'decoupling' .mdp parameters? They're there specifically for your type of
calculations.
Sander
On Sep 2, 2010, at 04:58 , Emanuel Birru wrote:
Hi,
I am doing a partition coefficient of solute between
Dear users,
Gromacs-4.5 is finally out and although all major and critical bugs have
been cleared, we are aware that there are probably many small issues
still left.
We would like to ask all users to go ahead and *heavy* test run the
code. For example,
* compile on different
Dear all,
so I downloaded Gromacs-4.5 and tried to compile the gpu-version with
cmake version 2.8.0 as stated in the gpu installation instructions as
export OPENMM_ROOT_DIR=/usr/local/openmm
cmake -DGMX_OPENMM=ON -DCMAKE_INSTALL_PREFIX=$HOME/GROMACS_4.5
make mdrun
make install-mdrun
But I
Today, I have made similar observations and recorded them in the Bugzilla
database here http://bugzilla.gromacs.org/show_bug.cgi?id=539
For now, I do not think cmake works properly. autotools have been fine for me,
however.
Mark
- Original Message -
From: Christian Mücksch
Hi,
Yes, cmake is broken:) We forgot to add some of the cmake specific files
for distribution (which is created using autoconf).
I'll release a 4.5.1 right now.
A very short lived 4.5 (RIP) :)
Rossen
On 9/2/10 11:23 AM, Christian Mücksch wrote:
Dear all,
so I downloaded Gromacs-4.5 and
On Sep 2, 2010, at 11:42 AM, Rossen Apostolov wrote:
Hi,
Yes, cmake is broken:) We forgot to add some of the cmake specific files for
distribution (which is created using autoconf).
I'll release a 4.5.1 right now.
Hi Rossen,
in ./src/tools/CMakeLists.txt the program gmx_rmsdist.c is
On 9/2/10 11:46 AM, Carsten Kutzner wrote:
On Sep 2, 2010, at 11:42 AM, Rossen Apostolov wrote:
Hi,
Yes, cmake is broken:) We forgot to add some of the cmake specific files for
distribution (which is created using autoconf).
I'll release a 4.5.1 right now.
Hi Rossen,
in
Hi,
Some CMake specific files were missing from the distributed tarball and
were breaking the build system. I've made a new release, 4.5.1, that
has a working CMake support. Nothing has changed for autoconf users.
Rossen
On 9/2/10 10:51 AM, Rossen Apostolov wrote:
Dear users,
Please keep all Gromacs-related correspondence on the gmx-users list. I am not
a private help service. I am CC'ing the message there; please continue any
discussion via the forum.
Creating a lipid bilayer is not a particularly easy task. You can generate a
leaflet by replicating the
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On 09/02/2010 12:37 PM, Rossen Apostolov wrote:
Hi,
Some CMake specific files were missing from the distributed tarball and
were breaking the build system. I've made a new release, 4.5.1, that
has a working CMake support. Nothing has changed
Dear Sir,
We have chosen force field Gromos96 53A6 parameter set.
In that forcefield, how we add this CA atom type.
Prabha
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before
Hi Prabha,
Why did you choose that force field, and what CA atom type?
Tsjerk
On Thu, Sep 2, 2010 at 1:30 PM, praba vathy sumipraba2...@gmail.com wrote:
Dear Sir,
We have chosen force field Gromos96 53A6 parameter set.
In that forcefield, how we add this CA atom type.
Prabha
--
Hi Florian,
What options did you give to cmake?
You have to specify the library name in FFTW3_LIBRARIES, not the lib
directory. E.g.
$ cmake ../gromacs-4.5.1
-DFFTW3F_LIBRARIES=/home/dommert/local/fftw3/lib/libfftw3f.so
Rossen
On 9/2/10 1:21 PM, Florian Dommert wrote:
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This is probably not intended for the list; it pertains directly to my membrane
tutorial and is likely a result of choosing the force field incorrectly or not
properly incorporating the lipid parameters as instructed.
-Justin
Tsjerk Wassenaar wrote:
Hi Prabha,
Why did you choose that
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On 09/02/2010 01:45 PM, Rossen Apostolov wrote:
Hi Florian,
What options did you give to cmake?
You have to specify the library name in FFTW3_LIBRARIES, not the lib
directory. E.g.
$ cmake ../gromacs-4.5.1
Hi Florian,
Thanks a lot! That was another miss. I have re-packaged 4.5.1 :) So if
someone has downloaded it in the last couple of hours, please
re-download it again (I know it's not the right thing to do with
releases though :-) )
Rossen
Hi Rossen,
thanks for this very helpful
Hi everyone,
I concatenated many trajectories with trjcat and didn't have any problem.
But when I did trjconv, I had this warning:
WARNING: Incomplete frame: nr 6077 time 12154
so I tried to do gmxcheck on my concatenated .xtc and got :
Reading frame 0 time0.000
# Atoms 192409
Hi,
I am using simulation for a membrane protein.
So i have downloaded the dppc.pdb along with it's topology files.
I have used the following steps for the simulation (Based on the link:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/01_pdb2gmx.html
).
We
Carla Jamous wrote:
Hi everyone,
I concatenated many trajectories with trjcat and didn't have any problem.
But when I did trjconv, I had this warning:
WARNING: Incomplete frame: nr 6077 time 12154
so I tried to do gmxcheck on my concatenated .xtc and got :
Reading frame 0 time
Make sure your gromacs is the latest version.
If not, update and try again.
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of praba vathy [sumipraba2...@gmail.com]
Sent: Thursday, September 02, 2010 9:06 PM
To:
praba vathy wrote:
Hi,
I am using simulation for a membrane protein.
So i have downloaded the dppc.pdb along with it's topology files.
I have used the following steps for the simulation (Based on the link:
#ZHAO LINA# wrote:
Make sure your gromacs is the latest version.
If not, update and try again.
The tutorial is specifically written for version 4.0.5, but will be compatible
with any version 4.5. Since the re-organization of the force field
directories, the information provided in the
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On 09/02/2010 02:56 PM, Rossen Apostolov wrote:
Hi Florian,
Thanks a lot! That was another miss. I have re-packaged 4.5.1 :) So if
someone has downloaded it in the last couple of hours, please
re-download it again (I know it's not the right
But it's a bit trivial to modify those things if you just following those steps
by steps.
Using the latest version can save lots of works.
By the way, thanks for the website, I once followed that too (nearly step by
step also).
Thanks with best regards,
lina
P.S actually you can upgrade your
On 9/2/10 3:21 PM, Florian Dommert wrote:
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On 09/02/2010 02:56 PM, Rossen Apostolov wrote:
Hi Florian,
Thanks a lot! That was another miss. I have re-packaged 4.5.1 :) So if
someone has downloaded it in the last couple of hours, please
-BEGIN PGP SIGNED MESSAGE-
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On 09/02/2010 03:39 PM, Rossen Apostolov wrote:
On 9/2/10 3:21 PM, Florian Dommert wrote:
On 09/02/2010 02:56 PM, Rossen Apostolov wrote:
Hi Florian,
Thanks a lot! That was another miss. I have re-packaged 4.5.1 :) So if
someone has
#ZHAO LINA# wrote:
But it's a bit trivial to modify those things if you just following those steps
by steps.
Using the latest version can save lots of works.
Indeed. But I'm also a fan of solving one problem at a time. A broken force
field file won't get fixed by trying to
For building membrane/protein systems I recommend charmm-gui.org
The server automatically builds the coordinates, which you should be
able to use
with any modeling program; CHARMM equilibration scripts are generated
as well
Krzysztof
On 9/2/10 6:20 AM, Justin A. Lemkul wrote:
Please
Dear Gromacs Users,
I am presently using gromacs4.5 beta(since I want implicit solvent). I wish to
apply intermolecular distance restraints.
To my surprise there is no merge option in pdb2gmx (although pdb2gnx -h, says
it has). So is there a new alternative to create intermolecular distance
nahren manuel wrote:
Dear Gromacs Users,
I am presently using gromacs4.5 beta(since I want implicit solvent). I
No need to use a beta version, the official 4.5 has been released.
wish to apply intermolecular distance restraints.
To my surprise there is no merge option in pdb2gmx
Hi,
I was wondering if anyone knows whether it is possible to restart a replica
exchange simulation if it stops during the run. I tried it once before and
got the error that all the replicas should be at the same time step for
replica exchange. When I checked the time step of different replicas,
HI
Residues PHE, TRP, TYR, and HIS are carrying Rings, or say pi bonds.
How does the Gromacs deal with polarity for all this four residues?
Is a single charge assigned for each atom on the center of atoms of the four
residues ?
Is pi bond given for the four residues in the force field?
Hi Chih-Ying Lin,
There's no such thing as a pi bond in a classical force field, bonds
are merely connections with a certain distance based potential.
Gromacs doesn't deal with polarity, the distribution of charges, etc.
is part of the force field. Better check the papers relating to the
force
2010/9/2 Luis Paulo luis...@gmail.com
Dear all
I need to calculate the normal modes of a protein. I am trying to generate
the hessian matrix with mdrun. But it did not generate the hessian matrix
(nm.mtx).
Thanks for some help
Luis Scott
--
Prof. Dr. Luis Paulo Scott
CMCC- Centro de
Dear Gromacs Users,
The problem actually is mine is a hexamer, ARBSCT (chains). I want RST to be
merged into a single molecular topology. I am either able to merge RS or ST or
RT but not the trimer as such.
I am able to do with -merge in the previous (ver 4.0.7 of ) pdb2gmx.
Best,
nahren
Luis Paulo wrote:
2010/9/2 Luis Paulo luis...@gmail.com mailto:luis...@gmail.com
Dear all
I need to calculate the normal modes of a protein. I am trying to
generate the hessian matrix with mdrun. But it did not generate the
hessian matrix (nm.mtx).
Thanks for some
nahren manuel wrote:
Dear Gromacs Users,
The problem actually is mine is a hexamer, ARBSCT (chains). I want RST
to be merged into a single molecular topology. I am either able to merge
RS or ST or RT but not the trimer as such.
How is the .pdb set up? Does it have both chain ID's and
- Original Message -
From: Nimesh Jain nimeshjain2...@u.northwestern.edu
Date: Friday, September 3, 2010 1:13
Subject: [gmx-users] Restart Replica Exchange
To: Discussion list for GROMACS users gmx-users@gromacs.org
Hi,
I was wondering if anyone knows whether it is possible to restart
The Bioinformatics Group at C-DAC, Pune is going to organize a Symposium on
Accelerating Biology from December 14-16 2010 at VITS, Pune. You can
register for the same at:
http://pune.cdac.in/html/events/bioinfo/accelerating_biology/index.aspx
Regards,
--
Anirban Ghosh
C-DAC, Pune, India
--
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