[gmx-users] Box in Implicit Solvent Simulations

[ifat shub]

Hi,
I am running simulations using implicit solvent. I am using the pbc = no
option in my mdp file, however, I see it the .gro file that gromacs is
creating a box for the system.What is the effect of the box in implicit
solvent simulations?

This is the mdp file that I am using:

------run.mdp------

integrator = md

nsteps = 20000

dt = 0.001

implicit_solvent = GBSA

pbc = no

nstlist = 0

ns_type = simple

rlist = 0

rgbradii = 0

coulombtype = Cut-off

rcoulomb = 0

vdwtype = Cut-off

rvdw = 0

tcoupl = v-rescale

tc_grps = system

tau_t = 0.1

ref_t = 1000

energygrps = Protein_chain_A Protein_chain_C Protein_chain_E
Protein_chain_G Protein_chain_I Protein_chain_K

gen_vel = yes

gen_temp = 1000

ld_seed = -1

gen_seed = -1

nstxout = 1

nstvout = 1

nstxtcout = 1

nstenergy = 1

------------------
Thanks,
Ifat

M.Sc. Student
Bar Ilan University
Ramat Gan
Israel
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