Ganesh CN wrote:
you can not use so many processors for such a small system in 3.3. In
4.0 you will be able to do it.
Thanks for your response David. Is it possible to scale up the
problem size so that I can run it on 16 or more processes ? If so,
could you let me know what parameter I have to change to scale up ?
(I am not too conversant with the molecular dynamics principles - so
please forgive my ignorance). Or is there is some other input file
which will work for 16 processes ? I am using cutoff.mdp as pasted
below :
use more water :)
title = dppc
cpp = /lib/cpp
integrator = md
nsteps = 5000
nstlist = 5
nstxout = 0
nstvout = 0
nstxtcout = 0
nstlog = 0
dt = 0.004
constraints = all-bonds
nstenergy = 0
ns_type = grid
coulombtype = cut-off
rlist = 0.9
rvdw = 1.4
rcoulomb = 1.4
tcoupl = berendsen
tc_grps = protein cl- sol
tau_t = 0.1 0.1 0.1
ref_t = 300 300 300
Pcoupl = no
Thanks,
Ganesh
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--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
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