Hi;
I've alreadyconverted the amber topology and coordinate files to gromacs
format.But when I want to start running theenergy minimization first by using
the grompp to generate .tpr file,I get this error:
Program gmx, VERSION5.0.2Source code
On 8/19/15 7:22 AM, anu chandra wrote:
Dear Gromacs users,
I just noticed that during simulation 'mdrun' writes gro file in two
formats - one with broken molecules at the boundaries and other one where
surface molecules are perfectly wrapped. Interestingly, this difference in
format depends
1. I am using it with CPMD as they have mentioned this version of gromacs
only.
2. The top-level force fields are not included as they are not present in
/usr/local/gromacs/share/top/ file for eg. BH4_oplsaa.itp, however its
there in the gmx-3.3.1_qmmm-1.3.2/share/top folder.
3. There is no
Hi,
I am unable to compile Gromamcs 5.1 using the following cmake command.
cmake .. -DGMX_FFT_LIBRARY=fftpack -DCMAKE_INSTALL_PREFIX=gromacs/gromacs-5.1
-DGMX_DOUBLE=off -DGMX_THREAD_MPI=off -DGMX_MPI=on
-DGMX_CPU_ACCELERATION=SSE4.1 -DGMX_USE_RDTSCP=off
Then I got the error message.
Boost =
Hi,
As the error says you should get a version =1.44 for the boost libraries
On 19/08/15 15:49, 岡部篤俊 wrote:
g minimal internal version. T
--
Felipe Merino
Max Planck Institute for Molecular Physiology
Department of Structural Biochemistry
Otto-Hahn-Str. 11
44227 Dortmund
Phone: +49 231 133
Sounds like a question for the acpype developers directly :-)
Mark
On Wed, Aug 19, 2015 at 8:52 AM Albert mailmd2...@gmail.com wrote:
Hello:
I am using acpype to create ligand topology. However, I noticed that
acpype may not recogonize Cl element which is a halogen atom correctly.
After
Hi,
On Wed, Aug 19, 2015 at 3:49 PM 岡部篤俊 atsutoshi0...@gmail.com wrote:
Hi,
I am unable to compile Gromamcs 5.1 using the following cmake command.
cmake .. -DGMX_FFT_LIBRARY=fftpack
-DCMAKE_INSTALL_PREFIX=gromacs/gromacs-5.1 -DGMX_DOUBLE=off
-DGMX_THREAD_MPI=off -DGMX_MPI=on
Hi;
I've alreadyconverted the amber topology and coordinate files to gromacs
format.But when I want to start running theenergy minimization first by using
the grompp to generate .tpr file,I get this error:
Program gmx, VERSION5.0.2Source code
Hi,
Please use a more recent GROMACS version, unless you are actually a
forensic archaeologist.
Mark
On Wed, Aug 19, 2015 at 1:58 PM Padmani Sandhu padmanisandh...@gmail.com
wrote:
Hello everyone,
I am trying to install gmx-3.3.1 on ubuntu 14.04. I have compiled it using
following
On 8/19/15 7:58 AM, Padmani Sandhu wrote:
Hello everyone,
I am trying to install gmx-3.3.1 on ubuntu 14.04. I have compiled it using
following commands:
Any reason you're using wildly outdated software?
./configure
make
sudo make install
*However the program was installed but while
Hi Ahmet,
Have you looked at the trajectories? Is the molecule really whole/centered?
Cheers,
Tsjerk
T
On Wed, Aug 19, 2015 at 3:32 PM, Ahmet Yıldırım ahmedo...@gmail.com wrote:
Dear users,
I am trying to get the conformational entropy of some structures but the
results I got are
Hello everyone,
I am trying to install gmx-3.3.1 on ubuntu 14.04. I have compiled it using
following commands:
./configure
make
sudo make install
*However the program was installed but while running grommp, it was
terminated with an error :*
checking input for internal consistency...
calling
Dear Gromacs users,
I just noticed that during simulation 'mdrun' writes gro file in two
formats - one with broken molecules at the boundaries and other one where
surface molecules are perfectly wrapped. Interestingly, this difference in
format depends on where I run the simulation - either in a
Hi,
CPUs and GPUs are not created equal, so there's not enough information to
say anything. But 3k atoms will not keep most GPUs fully busy, so you will
want to consider running multiple replicates of your system, e.g. with
mdrun -multi. See also http://arxiv.org/abs/1507.00898
Mark
On Tue, Aug
Dear users,
I am trying to get the conformational entropy of some structures but the
results I got are strange. I tried two methods. I removed jumps from
trajectory and centered the protein in box (1). I used the raw trajectory
(2). GROMACS gives different results for each processes. Which
Hi,
Yes, one chip on the dual chip K80 GPU (as long as it's cooled well) will
be roughly as fast as a K40 with GROMACS.
Otherwise, the setup looks well-balanced, it should give good performance
with GROMACS! Note that you can save money on:
- SSD which is not necessary for GROMACS production
Yeah sorry, I realized later that I did not read the complete thing...
Bad habit.
On 19/08/15 16:18, Mark Abraham wrote:
Hi,
No, the warning about Boost versions is unrelated and just happens to
precede the issue.
Mark
On Wed, Aug 19, 2015 at 4:13 PM Felipe Merino
Thank you, Mark. Got it.
Qing
At 2015-08-19 17:32:22, Mark Abraham mark.j.abra...@gmail.com wrote:
Hi,
You've observed a single event. By itself that doesn't mean much of
anything. If you were in a car crash today, that doesn't mean you will be
in one every time you go on the road. But if you
As far as I¹ve understood, the absolute distance reported using g_dist
(note: alternative name in 5+) and the reported harmonic potential between
two groups using pull code in grompp, doesn¹t always match.
As such, I some times end up with neighbouring umbrella histograms
practically sitting on
Nash, Anthony a.nash@... writes:
As far as I¹ve understood, the absolute distance reported using g_dist
(note: alternative name in 5+) and the reported harmonic potential between
two groups using pull code in grompp, doesn¹t always match.
As such, I some times end up with neighbouring
Helo guys!
I'm trying to compile Gromacs-5.1-rc1 with XLC 13.1.2 ESSL 5.3 and I'm
facing
an undefined reference error.
Here's what I got:
$ cd /home/ibm/crash/gromacs-agosto/2/gromacs-5.1-rc1/single/share/template
/usr/bin/cmake -E cmake_link_script CMakeFiles/template.dir/link.txt
--verbose=1
Hello,
I have a quite long continuous trajectory coming from several initial
input pieces (cluster crashed...) that I want to downsample, as a start
from 0.5ps timestep in the source files to just 1ps and later bigger
timesteps.
Using the -dt option of trjconv (GROMACS 4.6.5.), there seem to be
Line 52 of cmake/FindSphinx.cmake file is written below.
string(REGEX REPLACE Sphinx \\([^)]*\\) ([^ ]+) \\1
SPHINX_EXECUTABLE_VERSION ${SPHINX_VERSION_OUTPUT_VARIABLE})
Can you tell me how I can change the line?
Bests,
Leucer
2015/08/19 23:11、Mark Abraham mark.j.abra...@gmail.com のメッセージ:
Hi;
I've alreadyconverted the amber topology and coordinate files to gromacs
format.But when I want to start running theenergy minimization first by using
the grompp to generate .tpr file,I get this error:
Program gmx, VERSION5.0.2Source code
Hi;I've alreadyconverted the amber topology and coordinate files to gromacs
format.But when I want to start running theenergy minimization first by using
the grompp to generate .tpr file,I get this error:
Program gmx, VERSION5.0.2Source code
Hello:
I am using acpype to create ligand topology. However, I noticed that
acpype may not recogonize Cl element which is a halogen atom correctly.
After acpype, it generate a new ligand pdb file called: lig_NEW.pdb and
I found the following:
ATOM 10 C09 UNK Z 1 11.502 -10.939
Hi,
You've observed a single event. By itself that doesn't mean much of
anything. If you were in a car crash today, that doesn't mean you will be
in one every time you go on the road. But if you observe yourself in a car
crash every day, now you have evidence that you need driving lessons... If
Hi Anu,
Since .xtc doesn't store velocities, its a much more compact trajectory
than it's .trr counterpart, i.e. it has a smaller size. Also, .xtc is more
easier on your computer RAM than the .trr file, during visualizing or
analyzing using the .xtc trajectories.
If you are looking to save disk
Hi Anu,
Again that is up to you. I do not save a full precision file for my
analysis. In the infinite disk space (and time!) limit of course you
would like to have veolcities, forces, and positions of all atoms very
frequently. However, if you do not foresee any analysis requiring
velocities
Hi,
I did a 200-ns MD for a protein and found an interesting conformation
transition, and according to NMR study in literature, it is believed that 10 us
~ ms scale simulations are needed to get this conformation transition.
However, when I tried to reproduce this conformation transition, I was
Hello Justin,
I have copied both the .itp files which were giving error in to
/usr/local/gromacs/share/top using command:
sudo cp BH4_oplsaa.itp /usr/local/gromacs/share/top
sudo cp ffoplsaabon.itp /usr/local/gromacs/share/top
and now grompp worked. Please can you suggest me any solution so
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