[gmx-users] Negative average pressure value after NPT equilibration

Dario Akaberi dario.aka17 at gmail.com
Sat Oct 22 13:33:52 CEST 2016


Dear users

I am trying to perform the MD simulation of a protein in water using the
amberFF99sb-ildn force field.

To so so I created the protein topology specifying TIP3P water. then I
created a dodecahedron box with -d 1.0, I filled it using spc216.gro. and
added 7 NA ions. This resulted in a system of  8837 water molecules plus
the 7 ions and the protein. Minimization were carried out using conjugate
gradient method (gromacs is compiled with double precision) which converged
to emtol 0.01 in 48000 steps.The following nvt ensemble worked well (I
think) and the resulting average temperature was 299.702 (ref temperature
was 300 K) with Err. Est. = 0.32  RMSD 4.39922 and tot-Drift 1.58106.
Now the problems begin. After NVT equilibration I performed an NPT
equilibration step of 100 ps which resulted in an average pressure of -50.
I then tried to equilibrate for a longer time: 150 and 200 ps with the same
result. I also tried a 500 ps NPT equilibration which resulted in an
average  pressure of -60 and average density 998.935 with Err. Est = 0.12,
RMSD = 2.38 and Tot-Drift = 0.83 /kg/m^3).

This is the NPT.mdp file I used:

define                    = -DPOSRES
integrator               = md        ; leap-frog integrator
nsteps                   = 50000             ; 2 * 50000 = 100 ps
dt                          = 0.002        ; 2 fs

nstxout                   = 500        ; save coordinates every 1.0 ps
nstvout                   = 500        ; save velocities every 1.0 ps
nstenergy               = 500        ; save energies every 1.0 ps
nstlog                     = 500        ; update log file every 1.0 ps

continuation                = yes        ; Restarting after NVT
constraint_algorithm        = lincs            ; holonomic constraints
constraints                = all-bonds            ; all bonds (even heavy
atom-H bonds) constrained
lincs_iter                = 1                ; accuracy of LINCS
lincs_order                = 4                ; also related to accuracy

cutoff-scheme              = Verlet
ns_type                   = grid
nstlist                   = 10
rlist                       = 1.0
rcoulomb                = 1.0
rvdw                    = 1.0

coulombtype                = PME
pme_order                = 4
fourierspacing                = 0.16

; Temperature coupling is on
tcoupl                = V-rescale                    ; modified Berendsen
thermostat
tc-grps                    = Protein Non-Protein
tau_t                    = 0.1      0.1
ref_t                    = 300       300            ; reference
temperature, one for each group, in K

pcoupl                    = Parrinello-Rahman            ; Pressure
coupling on in NPT
pcoupltype                = isotropic                    ; uniform scaling
of box vectors
tau_p                    = 2.0                ; time constant, in ps
ref_p                    = 1.0                ; reference pressure, in bar
compressibility             = 4.5e-5                    ; isothermal
compressibility of water, bar^-1
refcoord_scaling            = com                          * I get an error
without this

; Periodic boundary conditions
pbc                    = xyz                ; 3-D PBC
; Dispersion correction
DispCorr                = EnerPres                    ; account for cut-off
vdW scheme
; Velocity generation
gen_vel                    = no                ; Velocity generation is off

I don't know what I'm doing wrong, and unfortunately, I am new to molecular
dynamics simulation which doesn't help. I tried to find a solution and
found some other cases where people had a negative pressure after NPT
equilibration step but it was like an average pressure of -2 not -60!
Any help would be very appreciated.

Thanks,

Dario


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