[gmx-users] the calculation time

[ahmet yıldırım]

Dear Justin and Mark,

I want to investigate the structure xxx.pdb. When I run "the run.mdp" the
gromac shows that will end in 25 days. What kind of changes do you recommend in
"the run.mdp file" to reduce/short the calculation time? Or, Is there any
error/missing in the file? My run.mdp input script is the following.

PC hardware:İntel Core I7 (four core), 6GB RAM

Thanks in advance

"The run.mdp"
title           = MD
cpp             = /usr/bin/cpp
constraints     = all-bonds
integrator      = md
dt              = 0.002    ; ps !
nsteps          = 10000000 ; total 20000 ps = 20 ns.
nstcomm         = 1
nstxout         = 100000    ; collect data every 200 ps
nstvout         = 100000
nstfout         = 0
nstlog          = 1000
nstenergy       = 1000
nstlist         = 10
ns_type         = grid
rlist           = 1.0
coulombtype     = PME
rcoulomb        = 1.0
vdw-type    = cut-off
rvdw            = 1.4
fourierspacing  = 0.12
pme_order       = 4
ewald_rtol      = 1e-5
optimize_fft    = yes
; Berendsen temperature coupling is on in two groups
Tcoupl          = berendsen
tc-grps         = Protein non-protein
tau_t           = 0.1 0.1
ref_t           = 300 300
; Energy monitoring
energygrps      = Protein non-protein
; Pressure coupling
Pcoupl          = berendsen
tau_p           = 1.0
compressibility = 5e-5 5e-5 5e-5 0 0 0
ref_p           = 1.0


-- 
Ahmet YILDIRIM
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