Hi Justin,
thanks a lot. I followed the link and modify rcon accordingly. The problem
was fixed.
Thank you once again.
Cheers,
/P
El sáb., 19 oct. 2019 a las 16:34, Justin Lemkul ()
escribió:
>
>
> On 10/18/19 6:35 AM, Patricia Saenz Méndez wrote:
> > Hi!
> > I am trying to run a simple MD
On 10/18/19 6:35 AM, Patricia Saenz Méndez wrote:
Hi!
I am trying to run a simple MD simulation as usual, but with this system I
have got the same error message:
*Fatal error:There is no domain decomposition for 160 ranks that is
compatible with thegiven box and a minimum cell size of
Hi!
I am trying to run a simple MD simulation as usual, but with this system I
have got the same error message:
*Fatal error:There is no domain decomposition for 160 ranks that is
compatible with thegiven box and a minimum cell size of 1.02425 nmChange
the number of ranks or mdrun option
Hi,
Thanks Mr. Bauer for your help. Actually, I was running grompp in
desktop and the mdrun in cray. Now I am running both in cray and it runs
fine.
Thanks again.
Dhrubajyoti Maji
On Mon, 10 Jun 2019 at 20:38, Paul bauer wrote:
> Hello,
>
> did you change the command to submit the
Hello,
did you change the command to submit the calculation or did you use a
different machine to run the calculations?
This error usually means that the domain decomposition can't run on the
requested number of (thread)-MPI ranks.
Try using a different number of ranks or different
Dear gromacs users,
I am studying a system of molten acetamide in GROMACS-2018.3. I
have run EM and then NPT equilibration of 5 ns. Here-under, everything is
fine but when I try to run a 50 ns NPT production run the following error
occurs :
There is no domain decomposition for 56 ranks
Deal all,
I am doing coarse-grained bonded and nonbonded parametrization using
votca-gromacs. The "mpirun -np 64 gmx_mpi mdrun" work fine till step_021 of
parametrization where it crashes because it can not find any domain
decomposition for 64 ranks that is compatible with the system size. Even it
On 11/29/17 5:43 PM, MD wrote:
Hi folks,
I got a fatal error when running em.mdp. Do you think if it is the .mdp
that is causing this issue?
My command line is : gmx mdrun -v -deffnm em
The Fatal error:
"There is no domain decomposition for 40 ranks that is compatible with the
given box
Hi folks,
I got a fatal error when running em.mdp. Do you think if it is the .mdp
that is causing this issue?
My command line is : gmx mdrun -v -deffnm em
The Fatal error:
"There is no domain decomposition for 40 ranks that is compatible with the
given box and a minimum cell size of 2.42098
Dear users,
I get "domain decomposition error" in the energy minimization step of an
apo-protein. The last part of the log file is below.
log file:
...
Initializing Domain Decomposition on 24 ranks
Dynamic load balancing: no
Will sort the charge groups at every domain (re)decomposition
Initial
Dear Users,
I am simulating a nanotube with bonds and LINCS = all-bonds. Because the
tube is bending I tried to apply bonds or LINCS constraints between atoms
lying oppositely within the circles (tube diameter) so I used just one to
check:
[ bonds ]
2485245117.465
And I get:
Can you please advise? With large constraints it does not work... with [
distance_restraints ] it works but only with mdrun -nt 1
my mdp:
disre= simple
disre-fc = 1000
integrator = md
tinit= 0.0
dt = 0.008
On 2/5/14, 10:46 AM, Steven Neumann wrote:
Can you please advise? With large constraints it does not work... with [
distance_restraints ] it works but only with mdrun -nt 1
my mdp:
disre= simple
disre-fc = 1000
integrator = md
tinit
Thank you. Can you specify what does long mean? Is there any limit?
On Wed, Feb 5, 2014 at 3:49 PM, Justin Lemkul jalem...@vt.edu wrote:
On 2/5/14, 10:46 AM, Steven Neumann wrote:
Can you please advise? With large constraints it does not work... with [
distance_restraints ] it works but
On 2/5/14, 10:58 AM, Steven Neumann wrote:
Thank you. Can you specify what does long mean? Is there any limit?
You can define whatever interactions you want, but the size of each DD cell will
be assigned based on that interaction. As the previous error message indicated,
the minimum DD
Maybe you know how do they keep nanotubes rigid then?
On Wed, Feb 5, 2014 at 3:58 PM, Steven Neumann s.neuman...@gmail.comwrote:
Thank you. Can you specify what does long mean? Is there any limit?
On Wed, Feb 5, 2014 at 3:49 PM, Justin Lemkul jalem...@vt.edu wrote:
On 2/5/14, 10:46 AM,
Depends on the size of your system and how much parallelism you want to
use. See manual section on DD.
Mark
On Wed, Feb 5, 2014 at 4:58 PM, Steven Neumann s.neuman...@gmail.comwrote:
Thank you. Can you specify what does long mean? Is there any limit?
On Wed, Feb 5, 2014 at 3:49 PM, Justin
Thanks a lot!
Steven
On Wed, Feb 5, 2014 at 4:05 PM, Justin Lemkul jalem...@vt.edu wrote:
On 2/5/14, 11:05 AM, Steven Neumann wrote:
Maybe you know how do they keep nanotubes rigid then?
Nope, sorry.
-Justin
On Wed, Feb 5, 2014 at 3:58 PM, Steven Neumann s.neuman...@gmail.com
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