[gmx-users] 3.3 parallel runs - Lincs/PME/sorting errors?
anoddlad at yahoo.com
Thu Feb 16 19:13:05 CET 2006
I'm still playing with the use of 3.3 with my lipid
systems. I've been trying to equilibrate a 257-lipid
patch of bilayer generated with genbox and a smaller
block of lipid. Obviously, it has big cavities around
the edges, so I wasn't expecting a flawless run.
However, examining a crashed trajectory made with 4
nodes showed that water molecules were mysteriously
clustering towards the centre of four blocks along the
x-axis. Is there some kind of maximum size of a
system, beyond which PME no longer works properly over
multiple processors? Could it be an error in
deshuffling? Or is it not a problem at all?
University of Bristol
details from .mdp file:
cpp = /lib/cpp
constraints = all-bonds
integrator = md
dt = 0.0015 ; ps !
nsteps = 10000 ; total 7500 ps.
nstcomm = 1
nstxout = 1000
nstvout = 1000
nstfout = 0
nstlog = 1000
nstenergy = 1000
nstlist = 10
ns_type = grid
coulombtype = PME
rlist = 1.5
rcoulomb = 1.5
rvdw = 1.5
pme_order = 8
fourierspacing = 0.2
optimize_fft = yes
; Berendsen temperature coupling is on in two groups
Tcoupl = berendsen
tc-grps = DOPC SOL
tau_t = 0.1 0.1
ref_t = 300 300
; Energy monitoring
energygrps = DOPC SOL
; Isotropic pressure coupling is now on
Pcoupl = berendsen
Pcoupltype = surface-tension
tau_p = 5
compressibility = 4.5e-5 4.5e-5
ref_p = 410 1.0
; Generate velocites is off at 300 K.
gen_vel = no
gen_temp = 300.0
gen_seed = 173529
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