[gmx-users] Energy Minimisation and Equilibration Problems

[Nancy]

Hello,

I am trying to run equilibration on my solvated ethylene glycol (ethanediol)
system.  I started with an ethanediol mol2 file from which topolbuild
generated various files.  I used editconf to enlarge to box of the
"ethanediol.gro" file:

$ editconf -f ethanediol.gro -o ethanediol_box.gro -box 5 5 5

and then I used genbox to solvate it:

$ genbox -cp ethanediol_box.gro -cs spc216.gro -shell 1 -o
ethanediol_solv.gro -p ethanediol.top

I ran energy minimisation on it:

$ grompp -f minim.mdp -c ethanediol_solv.gro -p ethanediol.top -o em.tpr

my minim.mdp file is:

==========================
define        = -DFLEXIBLE
integrator    = steep
emtol        = 1000.0
emstep          = 0.01
nsteps        = 5000

nstlist        = 1
ns_type        = grid
rlist        = 1.0
coulombtype    = PME
rcoulomb    = 1.0
rvdw        = 1.3
pbc        = xyz

pme_order    = 4
constraints     = none

nstxout        = 1
nstvout        = 1
nstenergy    = 1
nstlog        = 1
==========================

$ mdrun -v -deffnm em

and the energies converge (although I think that the values are still too
large for this system):

==========================
Steepest Descents converged to Fmax < 1000 in 12 steps
Potential Energy  = -1.1206108e+04
Maximum force     =  9.4016180e+02 on atom 31
Norm of force     =  3.4989252e+02
==========================

When I try to run equilibration with the following .mdp file:

==========================
title        = Ethanediol equilibration
define        = -DPOSRES
integrator    = md
nsteps        = 5000
dt        = 0.0002

nstxout        = 10
nstvout        = 10
nstenergy    = 10
nstlog        = 10

continuation    = no
constraint_algorithm = lincs
constraints    = all-angles
lincs_iter    = 1
lincs_order    = 4

ns_type        = grid
nstlist        = 5
rlist        = 1.0
rcoulomb    = 1.0
rvdw        = 1.3

coulombtype    = PME
pme_order    = 4
fourierspacing    = 0.16

tcoupl        = V-rescale
tc-grps        = EDO SOL
tau_t        = 0.1 0.1
ref_t        = 300 300

pcoupl        = no

pbc        = xyz

DispCorr    = EnerPres

gen_vel        = yes
gen_temp    = 300
gen_seed    = -1
==========================

the system "blows up".  Addtionally, the structure of the solute is
incorrect (all atoms are bonded to each other).

Please advise on how to minimise such a system further, and as to why the
equilibration is so unstable.

Thank you.

Nancy
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