[gmx-users] Problem with OpenMP+MPI
jalemkul at vt.edu
Wed Feb 27 16:33:28 CET 2013
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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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