Dear Sir,

Following energy minimization, NVT, and NPT simulations, I visualized the npt.gro file in VMD. Notably, an empty portion resembling a hole is evident within the acetone solvent box. Seeking guidance on addressing this issue.

em file

; minim.mdp - used as input into grompp to generate em.tpr

; Parameters describing what to do, when to stop and what to save

integrator = steep ; Algorithm (steep = steepest descent minimization)

emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm

emstep = 0.01 ; Minimization step size

nsteps = 50000 ; Maximum number of (minimization) steps to perform

; Parameters describing how to find the neighbors of each atom and how to calculate the interactions

nstlist = 1 ; Frequency to update the neighbor list and long range forces

cutoff-scheme = Verlet ; Buffered neighbor searching

ns_type = grid ; Method to determine neighbor list (simple, grid)

coulombtype = PME ; Treatment of long range electrostatic interactions

rcoulomb = 1.2 ; Short-range electrostatic cut-off

rvdw = 1.2 ; Short-range Van der Waals cut-off

pbc = xyz ; Periodic Boundary Conditions in all 3 dimensions

NVT

title = OPLS Lysozyme NVT equilibration

define = ; position restrain the protein

; Run parameters

integrator = md ; leap-frog integrator

nsteps = 50000000 ; 2 * 50000000 = 100000 ps

dt = 0.002 ; 2 fs

; Output control

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

; Bond parameters

continuation = no ; first 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 = 1.2 ; short-range electrostatic cutoff (in nm)

rvdw = 1.2 ; short-range van der Waals cutoff (in nm)

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 = system ; 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 = yes ; assign velocities from Maxwell distribution

gen_temp = 300 ; temperature for Maxwell distribution

gen_seed = -1 ; generate a random seed

NPT

title = OPLS Lysozyme NPT equilibration

define = ; position restrain the protein

; Run parameters

integrator = md ; leap-frog integrator

nsteps = 5000000 ; 2 * 5000000 = 10000 ps

dt = 0.002 ; 2 fs

; Output control

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

; Bond parameters

continuation = yes ; Restarting after NVT

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 scheme

rcoulomb = 0.5 ; short-range electrostatic cutoff (in nm)

rvdw = 0.5 ; short-range van der Waals cutoff (in nm)

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 = system ; 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 on

pcoupl = Berendsen

pcoupltype = isotropic

nstpcouple = -1

tau_p = 2.0 ; time constant, in ps

ref_p = 1.0 ; reference pressure, in bar

compressibility = 2.31943e-09 ; isothermal compressibility of acetone, bar^-1

refcoord_scaling = com

; Periodic boundary conditions

pbc = xyz ; 3-D PBC

; Velocity generation

gen_vel = no ; Velocity generation is off

Best regards,

LUKHMANUL HAKEEM K.