[gmx-users] Energy Minimisation and Equilibration Problems

[Bruce D. Ray]

On Wednesday, August 5, 2009 at 6:03:51 PM, Nancy <nancy5villa at gmail.com> wrote:
> 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
> ==========================

{remainder snipped}

The energies do seem large.  What happens if you do energy minimization
with emtol = 10.0  ?


-- 
Bruce D. Ray, Ph.D.
Associate Scientist, and Operations Director
NMR Center
IUPUI
Physics Dept.
402 N. Blackford St.
Indianapolis, IN  46202-3273


>
>From: Nancy <nancy5villa at gmail.com>
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Sent: Wednesday, August 5, 2009 10:28:47 PM
>Subject: [gmx-users] Energy Minimisation and Equilibration Problems
>


      
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