GROMACS version:

GROMACS modification: Yes/No

Greetings of the day!

I am running MD simulations of only the SPCE water box with a length of 20 x 20 x 20 angstroms at NVT ensembles. I calculated the density of water along the Z-axis. At the boundary (0 and 20 angstroms) the density (at first and last bins) is less than 1 g/cm^3. Please see the attached input file and density file, let me know where is wrong. I am expecting density at the boundaries also 1 g/cm^3. Any help is appreciated.

Thank you very much.

Best regards,

Nagaraju

Here is my input file:

########################################

title = Bulk Water (268 molecules) NVT equilibration

; Run parameters

integrator = md ; leap-frog integrator

nsteps = 5000000 ;1 * 5000 = 5000 ps (5 ns)

dt = 0.001 ; 1 fs

; Output control

nstxout = 50 ; save coordinates every 0.05 ps (50 fs)

nstvout = 50 ; save velocities every 0.05 ps (50 fs)

nstenergy = 50 ; save energies every 0.05 ps (50 fs)

nstlog = 50 ; update log file every 0.05 ps (50 fs)

nstxout-compressed = 50 ; save compressed coordinates every 10.0 ps

compressed-x-grps = System ; save the whole system

; Bond parameters

continuation = yes ; restarting dynamics run

constraint_algorithm = lincs ; holonomic constraints

constraints = h-bonds ; bonds involving H are constrained

lincs_iter = 1 ; accuracy of LINCS

lincs_order = 4 ; also related to accuracy

; Nonbonded settings

cutoff-scheme = Verlet ; Buffered neighbor searching

ns_type = grid ; search neighboring grid cells

nstlist = 10 ; 20 fs, largely irrelevant with Verlet

rcoulomb = 0.9 ; short-range electrostatic cutoff (in nm)

rvdw = 0.9 ; short-range van der Waals cutoff (in nm)

; Dispersion correction

DispCorr = EnerPres ; account for cut-off vdW scheme

; Electrostatics

coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics

pme_order = 4 ; cubic interpolation

fourierspacing = 0.16 ; grid spacing for FFT

; Temperature coupling is on

tcoupl = V-rescale ; modified Berendsen thermostat

tc-grps = SOL ; two coupling groups - more accurate

tau_t = 0.1 ; time constant, in ps

ref_t = 300 ; reference temperature, one for each group, in K

; Pressure coupling is off

pcoupl = no ; no pressure coupling in NVT

; Periodic boundary conditions

pbc = xyz ; 3-D PBC

; Velocity generation

gen_vel = no ; Velocity generation is off