Albert wrote:
Dear:
I am using gromacs for membrane simulation (under CHARMM36 FF) which
contains around 80,000 atoms. I've submitted over 200 CPU in the cluster
for such system with 2 fs time step. And what really astonished is that
the efficiency for such simulation is only 3ns/day..... I am wondering
what happen to my system or gromacs? What can I do to fasten the simulation?
Use fewer processors. You cannot necessarily assign a given system to an
arbitrary number of processors and expect linear performance increase with the
number of CPUs. At some point, the communication overhead exceeds any speedup
that might be obtained from using more CPUs. For 80k atoms, I would try some
benchmarks in the 64-96 CPU range to see how your performance is. My rule of
thumb is ~1000 atoms per CPU. There are considerations for PP:PME node ratio
when using DD, which also depend on the box type (see the Gromacs 4 paper and
the manual for more details on such details).
-Justin
here is my md.mdp:
/
title = god!
cpp = /usr/bin/cpp
include =
define =
integrator = md
dt = 0.001
nsteps = 100000000
nstxout = 1000000
nstvout = 1000000
nstlog = 1000000
nstenergy = 10000
nstxtcout = 100000
xtc_grps =
energygrps = Protein POPC SOL ION
nstcalcenergy = 1
nstlist = 1
nstcomm = 1
comm_mode = Linear
comm-grps = Protein_POPC Water_and_ions
ns_type = grid
rlist = 1.2
rlistlong = 1.4
vdwtype = Switch
rvdw = 1.2
rvdw_switch = 0.8
coulombtype = pme
rcoulomb = 1.2
rcoulomb_switch = 0.0
fourierspacing = 0.15
pme_order = 4
DispCorr = no
tcoupl = nose-hoover
nhchainlength = 1
tc-grps = Protein_POPC Water_and_ions
tau_t = 0.5 0.5
ref_t = 310 310
Pcoupl = parrinello-rahman
Pcoupltype = semiisotropic
tau_p = 5.0
compressibility = 4.5e-5 4.5e-5
ref_p = 1.0 1.0
pbc = xyz
gen_vel = no
optimize_fft = no
constraints = hbonds
constraint_algorithm = Lincs
/
Thank you very much
best
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
