[gmx-users] Energy Minimisation Values

[Bruce D. Ray]

On Wednesday, August 5, 2009 at 6:03:51 PM, Nancy <nancy5villa at gmail.com> wrote:
> 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 minimsation:
> 
> ==============================
> define        = -DFLEXIBLE
> integrator    = steep
> emtol        = 1000.0
> emstep          = 0.5
> nsteps        = 1000

I use more steps than 1000 (may want 10000) with:
     emstep               =  0.01
     nstcomm            =  1
     Tcoupl               =  no
     Pcoupl               =  no
     gen_vel             =  no

> 
> 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.


I use the same value of emtol, but that's just based on examples I've seen where
others have used that value.


-- 
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 6:03:51 PM
>Subject: [gmx-users] Energy Minimisation Values
>
>
>


      
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