Hi,

Even if there are minima on the surface that have negative energy (which
will depend how the model was developed, which you should look into)
there's no reason to expect an arbitrary starting configuration will find
one after a steepest descent search. A tangled pile of strings will stay
tangled.

Mark

On Fri, Feb 23, 2018, 23:28 Mahsa E <ebadi.ma...@gmail.com> wrote:

> 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
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