Nikit sharan wrote:
Dear justin,
As you suggested i have changed the coloumb type to PME and set
pme_order to 5 as said in the mailing list as it will increase the
Try an even number.
accuracy.But then the simulation is not getting completed.Its taking
hours together.Normally what's the running time for a lipid bilayer?I
Timings will be dependent on your hardware, especially the communication between
nodes in a cluster.
-Justin
dint find anything wrong with the topology as it is downloaded from
tielman's website.it is also well equilibriated.Kindly give me your
suggestions.My mdp.file is below:
title = Yo
cpp = cpp
include =
define =
integrator = md
tinit = 0
dt = 0.005
nsteps = 50000
init_step = 0
comm-mode = Linear
nstcomm = 1
comm-grps = system
nstxout = 200
nstvout = 0
nstfout = 0
nstcheckpoint = 1000
nstlog = 100
nstenergy = 100
nstxtcout = 1000
xtc-precision = 1000
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.0
domain-decomposition = no
coulombtype = PME
rcoulomb-switch = 0
rcoulomb = 1.0
epsilon-r = 1
vdw-type = Cut-off
rvdw-switch = 0
rvdw = 1.0
DispCorr = EnerPres
table-extension = 1
fourierspacing = 0.12
Pcoupl = berendsen
Pcoupltype = semiisotropic
tau_p = 0.5 0.5 0.5
compressibility = 4.5e-5 4.5e-5 4.5e-5
ref_p = 1.0 1.0 1.0
andersen_seed = 815131
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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