Hi Justin,
Thanks for your reply but am getting error suggesting a intermolecular
chemical bond is not allowed:
Program: gmx grompp, version 2016.4
Source file: src/gromacs/gmxpreprocess/convparm.cpp (line 649)
Fatal error:
The intermolecular_interaction can not contain chemically bonding
Hi,
Indeed, the standard way provided by CUDA to expose a subset of GPUs to an
application is the CUDA_VISIBLE_DEVICES (note the "S" ending); I did not
realize that is something you were interested in, I thought you wanted to
avoid using GPUs.
Also note (for anyone interested), a when using a
On 10/28/19 12:43 PM, Mustafa Tekpinar wrote:
Hello everybody,
I am trying to put a distance restraint between two atoms of different
molecules, such as DNA and RNA . I created an index file that contains only
these two atoms. Then, I called gmx genrestr with this index file. Now, I
have an
Hello everybody,
I am trying to put a distance restraint between two atoms of different
molecules, such as DNA and RNA . I created an index file that contains only
these two atoms. Then, I called gmx genrestr with this index file. Now, I
have an itp file, which includes a distance restraint.
Hi Paul,
I though you mean converting the .gro files to .xtc file using *trjcat *(which
was my initial question), sorry about that.
I see now, I just used *trjconv* to convert gro file them to .xtc files and
then ... .
.gro trjconv> .xtc --trjcat> .xtc(or trr)
Thanks
Alex
On
Hello,
I think I understood your problem (or at least hope so).
The issue is that it is no longer possible to directly concatenate text
based trajectory files, so I showed a possible way to work around the
problem.
You can also go back to a previous version of GROMACS to perform the
Hi Szilard,
I just found time to rerun the tests and your suggestion worked.
Many thanks for this.
Regards,
T.
On Wed, 16 Oct 2019 at 13:43, Szilárd Páll wrote:
> Hi,
>
> The issue is an internal error triggered by the domain decomposition not
> liking 14 cores in your CPU which lead to a
On 10/28/19 10:42 AM, Alex wrote:
Hi,
Paul,
I guess you understood the question wrongly. I have some *.gro files and I
want to concatenate them to have a trr (or xtc) trajectory.
I don't think Paul misunderstood at all. The version of trjcat that
you're using does not support an operation
Hi,
Paul,
I guess you understood the question wrongly. I have some *.gro files and I
want to concatenate them to have a trr (or xtc) trajectory.
Justin,
Yes indeed, It would be great if gmx trjcat could concatenate the gro files.
Regards,
Alex
On Mon, Oct 28, 2019 at 9:03 AM Justin Lemkul
On 10/28/19 6:26 AM, Paul bauer wrote:
Hello,
this looks like a case of misleading documentation. Can you file an
issue for this please on redmine.gromacs.org?
So that we don't forgot to fix this for the next patch release?
A possible work around for you can be that you first convert your
On 10/28/19 3:27 AM, Olga Press wrote:
Prof. Justin thanks so much for the explanation.
Why this phenomenon was not observed during the NVT equilibration when I
run a simulation of embedded protein?
A protein alone in water is surrounded by an isotropic medium that does
not exhibit the same
On 10/27/19 9:24 PM, Dave M wrote:
Hi All,
I am trying to define a bond between two molecules. Their parameters are
defined in separate itp files: molA.itp and molB.itp. I know I can
combine both the itp files but I am just wondering if I can define extra
bonds/angles joining two molecules
Hi,
Thanks, setting this variable allowed me to start GROMACS without errors
using the CPU.
The problem is that this method prevents me from using other free GPUs on
the host, but I would like to do this.
I also found out that setting the CUDA_VISIBLE_DEVICE variable to available
GPUs at the time
Dear Bidhan Chandra Garain,
Please share the log files of your benchmarks, that will help us better
identify if there is an issue and what the issue is.
Thanks,
--
Szilárd
On Mon, Oct 28, 2019 at 8:51 AM Bidhan Chandra Garain
wrote:
> Respected Sir,
> In my lab we have recently installed a
Hi,
Without any information about the parameters you are using in your
simulation, no one will be able to provide much help.
I recommend reading and understanding this tutorial before you try to
perform an umbrella simulation totally blind:
http://www.mdtutorials.com/gmx/umbrella/index.html
Hello,
this looks like a case of misleading documentation. Can you file an
issue for this please on redmine.gromacs.org?
So that we don't forgot to fix this for the next patch release?
A possible work around for you can be that you first convert your files
to e.g. XTC format, use trjcat to
Dear all,,
I am performing Umbrella sampling on a beeta-sheet to
determine the binding energy between them. I got the following error.
Fatal error:
Distance between pull groups 1 and 2 (4.908636 nm) is larger than 0.49 times
the box size (4.908511).
while the box-length after
Respected Sir,
In my lab we have recently installed a GPU Tesla V-100-PCIE, and installed
gromacs-2018.4. I tried to check its performance. I ran a job 128 dmpc lipid
simulation with 23453 atom in my lab cpu with 4 processor with 2 threading in
each processor. There it's performance is ~8
Prof. Justin thanks so much for the explanation.
Why this phenomenon was not observed during the NVT equilibration when I
run a simulation of embedded protein?
Do two equilibrations of NPT assemble, first with position restraint on the
protein (50ns) and second without restains (about 200ns) will
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