[gmx-users] Pressure very high with chloroform and gromacs-4.5.5

Nuno Azoia nazoia at gmail.com
Tue Oct 11 17:22:19 CEST 2011


I found something very strange while making a CHCl3 box using gromacs-4.5.5.
A look the mailing list, the manual and some release notes for
gromacs-4.5 and I couldn't found the answer for my problem. It's
possible that I'm doing something wrong, but I can not find what, so
I'm describe my problem.

I start a chloroform box from scratch, using genconf, and I get o
chloroform box with 1000 molecules. I get energy minimization without
Then I've run some equilibration steps in a NVT ensemble and in the
end I get pressure in the order of hundreds of bar. Then I change to
NPT conditions and both the pressure and the volume keep increasing
with time.

To discard the possibility of a size problem, I repeat everything with
a box of 27000 molecules, with a volume of ~13800 nm^3. The problem
was the same. Very high pressures (150-200 bar) and very low densities
(< 200 g/L) after 750 ps simulation time. And both volume and pressure
increasing with time.

I'm doing now the same procedure, but using gromacs-4.0.7 and I'm
getting very different (and better) results. After energy minimization
I run 50000 steps in a nvt ensemble and I got pressure around -30 bar
(Ok for me). After that I start to run the simulations in npt ensemble
and the pressure start to increase slowly, with negative values
because the system have very low densities (~400 g/L), and the volume
is decreasing. So I'm getting the normal reaction from the system.

Where is the problem? There are some different parameters to set in
the mdp file and I didn't realize that, or is this a problem in

In both cases I used this parameters:
integrator          =  md
dt                    =  0.002
nsteps              =  50000
nstcomm          =  1
nstxtcout           =  500
xtc-precision      =  1000
nstxout             =  0
nstvout             =  0
nstfout             =  0
nstlog              =  500
nstenergy           =  500

nstlist               =  5
ns_type             =  grid

;Reaction field
rlist               = 0.8
coulombtype         = Reaction-field
rcoulomb            = 1.4
epsilon_r           = 1.0
epsilon_rf          = 4.8
vdwtype             = cut-off
rvdw                = 1.4

; temperature coupling
Tcoupl              =  v-rescale
tc-grps             =  CHCL3
tau_t               =  0.05
ld_seed             =  -1
ref_t               =  300

; Energy monitoring
energygrps          =  CHCl3

; Isotropic pressure
Pcoupl              =  no
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
gen_seed            =  -1

lincs_order         =  4
lincs-warnangle     = 90
constraints         =  all-bonds

and of course, for the npt ensemble I just change
Pcouple     = berendsen

gen_vel      = no

Thank you in advance

Nuno Gonçalo Azoia Lopes

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