[gmx-users] Problem with OpenMP+MPI
shraban03 at gmail.com
Wed Feb 27 16:54:44 CET 2013
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
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??
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?
On Wed, Feb 27, 2013 at 10:33 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 2/27/13 10:25 AM, jesmin jahan wrote:
>> Thanks Justin.
>> Well, I am felling stupid now! Could you kindly provide me some better
>> .mdp parameters that make more sense?
>> gromacs 4.6 gives me error with my previous parameters which were
>> working perfect in gromacs 4.5.3
>> It says we have to use cut-off verlet, either we have to use coupling
>> temp or we have to set verlet-buffer-drift = -1.
>> Then it says set pbc to xyz or xy. I tried to change my rlist or other
>> cutoff values. It says box is too large or small.
>> So, i am really very confused!
>> It will be very kind of you, if you can suggest me some parameters
>> which match best with my previous parameters namely:
>>>> constraints = none
>>>> integrator = md
>>>> pbc = no
>>>> dt = 0.001
>>>> nsteps = 0
>>>> rcoulomb = 300
>>>> rvdw = 300
>>>> rlist = 300
>>>> nstgbradii = 300
>>>> rgbradii = 300
>>>> implicit_solvent = GBSA
>>>> gb_algorithm = HCT ;
>>>> sa_algorithm = None
>>>> gb_dielectric_offset = 0.02
>>>> optimize_fft = yes
>>>> energygrps = protein
> For implicit runs, I always set:
> pbc = no
> ns_type = simple
> comm-mode = angular
> rlist = 0
> rcoulomb = 0
> rvdw = 0
> nstlist = 0
> rgbradii = 0
> nstgbradii = 1
> coulombtype = cutoff
> vdwtype = cutoff
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> gmx-users mailing list gmx-users at gromacs.org
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Jesmin Jahan Tithi
PhD Student, CS
Stony Brook University, NY-11790.
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