GROMACS version: 2016-2018

GROMACS modification: Yes/No

Dear GMX users,

I know the implicit solvent function has been removed from the newer version, I recently need to run some Langevin simulations with implicit solvent.

I have Na+ and Cl- seperated at 2 nm in a vacuum box. For comparsion, I changed the “gb_epsilon_solvent” and extracted the force on Na atom as a function of the Na-Cl distance, but the relation seems to be unaffected by the choice of epsilon.

This doesn’t seem right, so I am asking if there is something I missed in my mdp file or how can I look at the different implicit solvent screening effect.

For reference, here are the mdp parameters I used:

#################################### INPUT ####################################

ld_seed = -1 ; Use random seed

tinit = 0 ; Initial time is 0

integrator = sd ; Langevin thermostat

dt = 0.002 ; Timestep (ps)

nsteps = 25000 ; Simulation duration (timesteps)

nstcomm = 250 ; Center of mass motion removal interval

comm_mode = linear ; Center of mass motion removal mode

ref_t = 300 ; System temperature (K)

gen_vel = yes ; Initialize velocities from Maxwellian distribution

tau_t = 2.0 ; Thermostat time constant (ps)

tc_grps = system ; Apply thermostat to complete system

############################## IMPLICIT SOLVENT ###############################

implicit_solvent = GBSA ; Generalized Born implicit solvent

gb_algorithm = OBC

rgbradii = 0 ; Cutoff for Born radii calculation (A)

gb_epsilon_solvent = 10 ; dielectric constant of implicit solvent

nstgbradii = 0

gb_dielectric_offset = 0.009

gb_saltconc = 0 ; Salt Concentration

gb_obc_alpha = 1

gb_obc_beta = 0.8

gb_obc_gamma = 4.85

sa_algorithm = Ace-approximation

sa_surface_tension = 2.25936

cutoff_scheme = group ; Method of managing neighbor lists

pbc = no ; Periodic boundary conditions disabled

coulombtype = cut-off ; Calculate coulomb interactions using cutoff

rcoulomb = 0 ; Coulomb cutoff of infinity

vdw_type = cut-off ; Calculate van der Waals interactions using cutoff

rvdw = 0 ; Van der Waals cutoff of infinity

rlist = 0 ; Neighbor list cutoff

nstlist = 0 ; Do not update neighbor list

nstlog = 50 ; Log output interval (timesteps)

nstenergy = 50 ; Energy output interval (timesteps)

nstcalcenergy = 50 ; Energy calculation interval (timesteps)

nstxout = 50 ; Trajectory output interval (timesteps)

nstvout = 50 ; Velocity outout interval (timesteps)

nstfout = 50 ; Force output interval (timesteps)

Thank you for any suggestion!

Shi