I don't think this is a sysconf issue. As you seem to have 16-core (hw
thread?) nodes, it looks like sysnconf returned the correct value
(16), but the OpenMP runtime actually returned 1. This typically means
that the OpenMP runtime was initialized outside mdrun and for some
reason (which I'm not
On a second thought (and a quick googling), it _seems_ that this is an
issue caused by the following:
- the OpenMP runtime gets initialized outside mdrun and its threads
(or just the master thread), get their affinity set;
- mdrun then executes the sanity check, point at which
omp_get_num_procs(),
Hi,
Has anybody tried g_tune_pme on stampede before? It appears stampede only
support ibrun, but not mpi -np type of stuff. So I assume one could launch
g_tune_pme with mpi using command like this (without -np option),
Ibrun g_tune_pme -s cutoff.tpr -launch
Unfortunately, it failed. Any
Dear gromacs users
I read the tutorial of umbrella sampling and have a small question I don't know
I do a umbrella samping simulation as the tutorial show us, the pmf image also
like the tutorial result .
But I was read another papers like the explain paper of g-wham: JCTC 2010.6
3713-3720.
On 12/5/14 10:54 PM, vg wrote:
Dear gromacs users
I read the tutorial of umbrella sampling and have a small question I don't know
I do a umbrella samping simulation as the tutorial show us, the pmf image also
like the tutorial result .
But I was read another papers like the explain paper
Hi all,
I am trying to run REST in GROMACS following the way proposed by tsuyoshi
terakawa. In their method,they implemented REST by rescaling the force-field
parameters without even changing the code. I have also searched in the mailing
list and found that we can manipulate the scale parameter
