[gmx-users] Energy Minimisation Values

Nancy nancy5villa at gmail.com
Thu Aug 6 00:03:51 CEST 2009


I was trying to run equilibration on my solvated ethylene glycol system.
However, the system seems to be "exploding".  I believe this is due to
inadequate energy minimisation, however, I am unable to minimise my system
any further.  I am using the following .mdp file "minim.mdp" for

define        = -DFLEXIBLE
integrator    = steep
emtol        = 1000.0
emstep          = 0.5
nsteps        = 1000

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

pme_order    = 4
constraints     = none

I process it with grompp, where "ethanediol_solv.gro" is the solvated
system, and "ethanediol.top" is the topolgy generated with topolbuild:

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

I then run it:

$ mdrun -v -deffnm em

mdrun outputs the following information:

Steepest Descents did not converge to Fmax < 1000 in 1001 steps.
Potential Energy  = -6.7546914e+03
Maximum force     =  2.7262363e+04 on atom 34
Norm of force     =  2.5032930e+03

I have viewed the output trajectory of the minimisation and I can see that
the waters do not move much.  I am wondering if there is a way to let
solvent water molecules move about during minimsation, and/or how to remove
some of them.  I am also unsure what value of emtol is reasonable for this
type of small system.

Please advise


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