[gmx-users] Energy Minimisation Values

[Justin A. Lemkul]

Nancy wrote:
> I tried decreasing emstep, and also tried increasing the number of 
> steps, but I still get the following output from mdrun:
> 
> ==================================================
> Steepest Descents did not converge to Fmax < 1000 in 5001 steps.
> Potential Energy  = -6.9329155e+03
> Maximum force     =  2.1965221e+04 on atom 39
> Norm of force     =  2.1487129e+03
> ==================================================
> 
> Please advise on how to further decrease the forces.
> 

Figure out what's pushing on atom 39 to generate such a huge force.  How to 
resolve the problem depends on what's happening.  If it's just a poorly-placed 
water molecule, you can try deleting that water molecule and trying again. 
Beyond that, it will depend on what you find.

-Justin

> Thanks,
> 
> Nancy
> 
> 
> 
> On Wed, Aug 5, 2009 at 6:08 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Nancy wrote:
> 
>         Hello,
> 
>         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
> 
>         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 think this is the root of your problem.  The maximum force is far
>     too high. Decrease your value of emstep (the default of 0.01 is
>     generally fine), and try again.  You will not likely see large
>     changes over the course of the trajectory.  EM makes small changes
>     to optimize geometry, hydrogen bonding, etc.  There are no dynamics
>     (remember that EM is essentially conducted at 0 K).
> 
>     -Justin
> 
>         Please advise
> 
>         Thanks
> 
>         Nancy
> 
> 
> 
> 
>         ------------------------------------------------------------------------
> 
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> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================