[gmx-users] Positive potential energy

[Mahsa]

Dear Mark,

Thank you for your reply. However, this is not clear for me yet since I
read this in the tutorial from Justin:

"There are two very important factors to evaluate and determine if EM was
successful. The first is the potential energy (printed at the end of the EM
process, even without -v). Epot should be negative. The second important
feature is the maximum force, Fmax, the target for which was set in
minim.mdp - "emtol = 1000.0" - indicating a target Fmax of no greater than
1000 kJ mol-1 nm-1."

So I don't know whether it is correct to continue a simulation which gives
positive potential energy after the energy minimisation or not?

And also as I mentioned in my first post (the two different mdp files), I
don't know if I should consider pbc or not, in my simulation.

Unfortunately, I didn't understand your answer to my previous questions. Do
you mean that the steep integrator is not good to do energy minimization
for this type of simulation?

Would you please help me to fix these problems?

Regards,
Mahsa

On Sat, Feb 24, 2018 at 8:54 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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.mahsa at 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
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>