[gmx-users] mdrun halting

varsha gautham varsha.gautham88 at gmail.com
Mon Feb 23 08:13:31 CET 2009


Dear all,

The production run of DPPC bilayer with 128 lipids and 3655 water and
some solvent molecules is halting without completion.As justin
suggested ,i changed the columb type from cut-off to PME.It keeps on
running for hours together.The system is well equilibriated and i
found no issues or warnings with starting structure.But still i dont
know why the production run is not getting completed.I hereby attached
mdp file.Please suggest me which parameter do i need to correct,

--------------------------------------
title           = cla
cpp             = cpp; the c pre-processor
constraints     = all-bonds
integrator      = md
dt              = 0.002 ; ps !
nsteps          = 2500 ; total 50 ps.
nstcomm         = 1
nstxout         = 2500 ; collect data every 1 ps
nstvout         = 0
nstfout         = 0
nstlist         = 10
ns_type         = grid
rlist           = 1.4
coulombtype     = PME
rcoulomb        = 1.4
rvdw            = 1.4
fourierspacing  = 0.12
fourier_nx      = 0
fourier_ny      = 0
fourier_nz      = 0
pme_order       = 4
ewald_rtol      = 1e-5
optimize_fft    = yes
; Berendsen temperature coupling is on in two groups
Tcoupl          = berendsen
tau_t           = 0.1 0.1
tc-grps         = DPPC SOL
ref_t           = 300 300
; Pressure coupling is on
Pcoupl          = berendsen
pcoupltype      = isotropic
tau_p           = 0.5
compressibility = 4.5e-5
ref_p           = 1.0
; Generate velocites is on at 300 K.
gen_vel         = yes
gen_temp        = 300.0
gen_seed        = 173529

thanks in advance.

-varsha



More information about the gromacs.org_gmx-users mailing list