On Fri, Jul 31, 2015 at 8:56 PM, Justin Lemkul jalem...@vt.edu wrote:
Particle decomposition was removed from the code a long time ago. There are
lots of places where work is split among threads.
Interesting. Now I've got some catching up to do with the
documentation and code.
Thanks,
On 7/30/15 3:14 PM, Elton Carvalho wrote:
On Thu, Jul 30, 2015 at 1:34 PM, Justin Lemkul jalem...@vt.edu wrote:
There are as many DD cells as there are (thread-)MPI processes. These can
be further subdivided into multiple OpenMP threads. What I was talking
about above is the use of only
On Thu, Jul 30, 2015 at 1:34 PM, Justin Lemkul jalem...@vt.edu wrote:
There are as many DD cells as there are (thread-)MPI processes. These can
be further subdivided into multiple OpenMP threads. What I was talking
about above is the use of only OpenMP, e.g.
mdrun -ntmpi 1 -nt X
There is
On Thu, Jun 25, 2015 at 7:39 PM, Justin Lemkul jalem...@vt.edu wrote:
On 6/25/15 2:46 PM, John Degenstein wrote:
I suppose in retrospect that I could simply use a single processor which I
think would reduce the number of DD cells and thus prevent this error.
Or just use OpenMP
Justin,
Thanks for the response, I have started to use pure OpenMP parallelization
which has solved the issue with DD. Somehow I missed this detail about
domain decomposition when reading about parallelization with tMPI vs OpenMP.
John
On Thu, Jun 25, 2015 at 6:39 PM, Justin Lemkul
Justin,
Ok, so I decided to take a different path to solve this issue. Essentially,
using the Berendsen Pcoupl the system should condense under high pressure.
For some reason it does not seem to work very quickly at least. To get
around this issue I running several steps of equilibration EM
On 6/25/15 2:46 PM, John Degenstein wrote:
Justin,
Ok, so I decided to take a different path to solve this issue. Essentially,
using the Berendsen Pcoupl the system should condense under high pressure.
For some reason it does not seem to work very quickly at least. To get
around this issue I
Hello,
I am trying to build a bigger liquid phase (1000) from a small cluster of
molecules (125). So far I have succeeded in forming the small cluster of
125 molecules shown in the below image. This was after running gmx trjconv
... -pbc cluster -center to bring the molecules into the middle of
