[gmx-users] Energy Minimisation Values

[Nancy]

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.

Thanks,

Nancy



On Wed, Aug 5, 2009 at 6:08 PM, Justin A. Lemkul <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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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