[gmx-users] Question about NVT

Justin Lemkul jalemkul at vt.edu
Sat Dec 2 06:07:48 CET 2006

Hello all,

I have a quick question regarding an MD simulation I am attempting to run
(again, the membrane protein which I had problems with previously).  Thanks to
the helpful suggestions; my system is now well-minimized!  The last step before
I would like to take before running full-out MD on my system is to equilibrate
my solvent and ions over a short timeframe (100ps).  My initial attempts have
been unsuccessful; the equilibration proceeds nicely for 960 steps (1.920 ps)
before I get a screen full of LINCS warnings.  Apparently one of my DPPC
molecules is being blown apart.  I have placed position restraints on both my
protein and my bilayer, in order to allow the solvent and ions (Na+) to move
around them.  I have attached my equil.mdp file below, in case I am making any
obvious mistakes.  I am piecing my .mdp file together from several examples and

My value for nstlog is set very small so I could monitor energies, etc after the
first failure...in case anyone was wondering :)

Thanks in advance for your kind advice in helping out a newbie.


PS - I'm running Gromacs v3.3 on Mac OSX v10.4.8, in case any of that matters.

title                    = MD  equilibration of solvent and ions
cpp                      = /usr/bin/cpp
include                  = -I./
integrator               = md
nsteps                   = 50000
nstlist                  = 10
nstxout                  = 1000
nstvout                  = 1000
nstlog                   = 10
nstenergy                = 1000
nstxtcout                = 1000
dt                       = 0.002
ns_type                  = simple
coulombtype              = cut-off
rlist                    = 0.9
rvdw                     = 0.9
rcoulomb                 = 0.9
fourierspacing           = 0.12
; Temperature coupling is on in four groups
tcoupl                   = berendsen
tc_grps                  = Protein DPPC SOL NA+
tau_t                    = 0.1 0.1 0.1 0.1
ref_t                    = 323 323 323 323
; Pressure coupling is not on
Pcoupl			 = no
ref_p			 = 1.0
gen_vel                  = no
gen_temp                 = 323
constraints               = all-bonds
constraint_algorithm     = lincs
optimize_fft             = yes
DispCorr                 = EnerPres
pbc			 = full

Justin A. Lemkul
Department of Biochemistry
Virginia Tech

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