On 2/27/13 11:27 AM, jesmin jahan wrote:
Thanks again Justin,
I added
cutoff-scheme = group
But still I am getting
OpenMP threads have been requested with cut-off scheme Group, but
these are only supported with cut-off scheme Verlet
which really says, openmp threads are supported only in Verlet!
Then you need to run without OpenMP threads.
-Justin
constraints = none
integrator = md
cutoff-scheme = group
pbc = no
;verlet-buffer-drift = -1
dt = 0.001
nsteps = 0
ns_type = simple
comm-mode = angular
rlist = 0
rcoulomb = 0
rvdw = 0
nstlist = 0
rgbradii = 0
nstgbradii = 1
coulombtype = cutoff
vdwtype = cutoff
implicit_solvent = GBSA
gb_algorithm = HCT ;
sa_algorithm = None
gb_dielectric_offset = 0.02
optimize_fft = yes
energygrps = protein
Best Regards,
Jesmin
On Wed, Feb 27, 2013 at 10:57 AM, Justin Lemkul <jalem...@vt.edu> wrote:
On 2/27/13 10:54 AM, jesmin jahan wrote:
Many thanks to you Justin for your help.
Now my .mdp file looks like:
constraints = none
integrator = md
pbc = no
verlet-buffer-drift = -1
dt = 0.001
nsteps = 0
ns_type = simple
comm-mode = angular
rlist = 0
rcoulomb = 0
rvdw = 0
nstlist = 0
rgbradii = 0
nstgbradii = 1
coulombtype = cutoff
vdwtype = cutoff
implicit_solvent = GBSA
gb_algorithm = HCT ;
sa_algorithm = None
gb_dielectric_offset = 0.02
optimize_fft = yes
energygrps = protein
And when I run mdrun, it says
"OpenMP threads have been requested with cut-off scheme Group, but
these are only supported with cut-off scheme Verlet"
Now if I add
cutoff-scheme = Verlet
It says
With Verlet lists only full pbc or pbc=xy with walls is supported
With Verlet lists nstlist should be larger than 0
So, what is the solution??
Use the group cutoff scheme rather than Verlet, otherwise we wind up right
back where we were before.
Also, you told me
"Note that implicit solvent calculations can be run on no more than 2
processors. You'll get a fatal error if you try to use more."
Is there any documentation for this? Can I cite you if I want to add
this information in an article?
It's a bug, listed on Redmine somewhere. I doubt that requires any sort of
citation, but if anyone asks, there are discussions in the list archive and
on redmine.gromacs.org.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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