Hi everybody,
I am working with electrolytes simulations using Gromacs, so I am trying to
get the residence time (ion pair lifetime, ion cage lifetime) of the ions.
I tried to use gmx hbond with the option -contat, but if try get the acf of
the interaction the program always has a crash, I also
hi guys,
from time to time i'm faced with GMX output files during MD called, e.g. in the
current case:
step8164372b_n254.pdb
step8164372b_n2.pdb
step8164372c_n254.pdb
step8164372c_n2.pdb
what i know is that they are related to kind of exploding systems. however, i'm
not really able to
On 9/6/17 3:46 PM, Deep kumar wrote:
Dear All,
I have produced the "ITP" files of the ligands using ATB server. I am
mentioning the steps here, please let me know if you think anything is
wrong.
a) uploaded the coordinates of ligand "RND" on ATB server. I chose
"heteromoelcule" molecule
Dear All,
I have produced the "ITP" files of the ligands using ATB server. I am
mentioning the steps here, please let me know if you think anything is
wrong.
a) uploaded the coordinates of ligand "RND" on ATB server. I chose
"heteromoelcule" molecule type.
b) Entered the "net charge" by
Dear All,
I have produced the "ITP" files of the ligands using ATB server. I am
mentioning the steps here, please let me know if you think anything is
wrong.
a) uploaded the coordinates of ligand "RND" on ATB server. I chose
"heteromoelcule" molecule type.
b) Entered the "net charge" by
Hi Ghosh,
Thanks for your answer.
But I'm not sure if I understood what you meant.
I already used insert-molecules command to create a box with the cationic
species.
Now, should I use the same command to include the anionic species into the
box?
Best
*Prof. Dr. Ednilsom OrestesDepartamento de
Dear GROMACS users,
I would like to perform non-equilibrium simulation adding a shear flow on
the liquid in my bio-membrane system composed of lipids and water. By means
of the applications of the deformations I would like to shear a water in
X-Y dimensions along the surface of the membrane.
On 9/6/17 5:36 AM, Seera Suryanarayana wrote:
Dear gromacs users,
I have gone through one gromacs tutorial of md simulation in solvent. Where
they mentioned that successive removal of position restrain. In other words
first they have done NPT ensemble with 1000 1000 1000 energy constants,
On Wed, Sep 6, 2017 at 5:36 AM, Seera Suryanarayana
wrote:
> Dear gromacs users,
>
> I have gone through one gromacs tutorial of md simulation in solvent. Where
> they mentioned that successive removal of position restrain. In other words
> first they have done NPT ensemble
On Wed, Sep 6, 2017 at 4:58 AM, Alex wrote:
> Hi all,
>
> We just got the new machines that were actually built with Szilárd's
> advice (a while back) and I am doing some preliminary tests. "My" machine
> has two 22-core Xeon E5 CPUs (44 cores / 88 threads total) + 3 Titan
Thanks, Pall,
I thought more threads will make the simulation faster. Is it not the case
for Gromacs?
I have tried to change the values. The file is provided here,
https://drive.google.com/a/rug.nl/file/d/0B-VoMAn-UrjYeko4d1VwUURCb00/view?usp=sharing
.
The command line is "gmx_mpi_d mdrun -s
First, take my wow!!! thats a huge system.
I would try the combinations of ntmpi XX and ntomp XXX for better
performance. Currently with 3 x GPU 1070 for ~11 K system im getting
around 50 ns/day (12 core processor).
So I guess you can fly here. :)
--
Gromacs Users mailing list
* Please
Well to better understand what is going on I suggest:* use strict; line tells
to search for possible problems even if script can go on like it is.Maybe just
remove it?
* remove &>/dev/null or even better use other file instead of /dev/null like
dump.txt
You will see it that system call is all
Dear gromacs users,
I have gone through one gromacs tutorial of md simulation in solvent. Where
they mentioned that successive removal of position restrain. In other words
first they have done NPT ensemble with 1000 1000 1000 energy constants,
then re executed the NPT ensemble with 100 100
Hi all,
We just got the new machines that were actually built with Szilárd's
advice (a while back) and I am doing some preliminary tests. "My"
machine has two 22-core Xeon E5 CPUs (44 cores / 88 threads total) + 3
Titan Xp GPUs. So far, I got good test system performance (~11K atoms,
92
Hello Vytautas,
I changed the script file to
gmx_mpi_d distance -s md_pull.tpr -f conf${i}.gro -n index.ndx -oall
dist${i}.xvg -select \'com of group \"lig\" plus com of group \"protein\"\'
rest is same
but it showed the same error as previous one.
Error
readline() on closed
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