I am trying to simulate the membrane patch of 5 lipid mixture obtained from the CHARMM-GUI (I edited the output README file as 1 to 20 for getting a total of 20 ns production run, and all simulations are done with single precision gromacs 5.0.4). With the default parameters, when I analyzed the last 5 ns trajectory , I found vary strange results for pressure and density as average pressure was found 1.6 bar and the average density of the water was found 1049 kg/m3.

So, do I need more longer simulation for the convergence of pressure and density to the reference values or I am doing something wrong.

mdp parameter file

integrator = md

dt = 0.002

nsteps = 500000

nstlog = 1000

nstxout = 5000

nstvout = 5000

nstfout = 5000

nstcalcenergy = 100

nstenergy = 1000

;

cutoff-scheme = Verlet

nstlist = 20

rlist = 1.2

coulombtype = pme

rcoulomb = 1.2

vdwtype = Cut-off

vdw-modifier = Force-switch

rvdw_switch = 1.0

rvdw = 1.2

;

tcoupl = Nose-Hoover

tc_grps = NPROT SOL_ION

tau_t = 1.0 1.0

ref_t = 310.15 310.15

;

pcoupl = Parrinello-Rahman

pcoupltype = semiisotropic

tau_p = 5.0 5.0

compressibility = 4.5e-5 4.5e-5

ref_p = 1.0 1.0

;

constraints = h-bonds

constraint_algorithm = LINCS

continuation = yes

;

nstcomm = 100

comm_mode = linear

comm_grps = NPROT SOL_ION

;

refcoord_scaling = com