[gmx-users] Energy Minimisation Values
nancy5villa at gmail.com
Thu Aug 6 00:26:09 CEST 2009
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.
On Wed, Aug 5, 2009 at 6:08 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> Nancy 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
>> 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
> Please advise
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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
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
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