[gmx-users] Positive potential energy

[Mahsa E]

Hello,

I want to simulate a box of polymer (32 chains) with salt. I started with
one chain of the polymer in the box. However, after the energy
minimisation, the energy is still positive. I found the discussion in the
link below very similar to the problem I have:

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users
/2017-February/111219.html

and tried the tips from Justin in the link but I still get positive energy.

This is my first MDP file:

define                   =
integrator               = steep
nsteps                   = -1
nstcgsteep               = 10
constraints              = none
lincs_order              = 8
emtol                    = 20
emstep                   = 0.01
comm-mode                = Linear
nstcomm                  = 1
nstcalcenergy            = 1
; Output frequency for energies to log file and energy file
nstlog                   = 1
nstenergy                = 1
ns_type                  = grid
cutoff-scheme            = verlet
coulombtype              = PME
nstlist                  = 10
rlist                    = 1.0
rcoulomb                 = 1.0
rvdw                     = 1.0
Tcoupl                   = no
Pcoupl                   = no
gen_vel                  = no
nstxout                  = 1
pbc                      = xyz

and this is the second one which I tried to follow the tips from the link
mentioned  above:

define                   =
integrator               = steep
nsteps                   = -1
nstcgsteep               = 10
constraints              = none
lincs_order              = 8
emtol                    = 20
emstep                   = 0.01
comm-mode                = Linear
nstcomm                  = 1
nstcalcenergy            = 1
; Output frequency for energies to log file and energy file
nstlog                   = 1
nstenergy                = 1
ns_type                  = grid
cutoff-scheme            = group
coulombtype              = cut-off
nstlist                  = 0
rlist                    = 0
rcoulomb                 = 0
rvdw                     = 0
Tcoupl                   = no
Pcoupl                   = no
gen_vel                  = no
nstxout                  = 1
pbc                      = no

My questions are:

- I'm not sure if either of these MDP files are correct for the system I'm
trying to simulate?

- Why energy is positive in this simulation? Is there something
fundamentally wrong in the simulation which I'm not aware of?

Regards,
Mahsa