[gmx-users] OPLS force field issue....

Justin Lemkul jalemkul at vt.edu
Wed Feb 5 03:58:03 CET 2014

On 2/4/14, 9:43 PM, Sidath Wijesinghe wrote:
> yes it worked. i only added CA CA CZ CZ 0.000 0.000 0.000 0.000 in diheadral
> block. since  all 12 errors point the same kind of diheadral type.

How did you decide these parameters were appropriate?  You're essentially saying 
that the rotational barrier to this dihedral is zero, so it is free to do 
anything it likes without consequence.  That's as useful as deleting the 
dihedral entirely.

> Then i tried to mdrun...i got this error message....
> Fatal error:
> 1 particles communicated to PME node 6 are more than 2/3 times the cut-off out
> of the domain decomposition cell of their charge group in dimension y.
> This usually means that your system is not well equilibrated.
> so i followed the  energy minimization steps given in the lysozyme tutorial...
> and ended up with vales like below...
>   Steepest Descents converged to Fmax < 1000 in 56 steps
> Potential Energy  =  8.3839850e+02
> Maximum force     =  9.7320355e+02 on atom 206
> Norm of force     =  1.8842863e+02
> there you have clearly stated that the potential energy should be in range of
> e-5 to e-6. but mine is ~+1000. i played with emsteps and
> nsteps. but still am getting the same potential energy.

For a condensed-phase system of an average protein in water, yes, the potential 
energy I report there is fairly typical.  Don't try to extrapolate this 
information too far.  For a condensed phase system, the potential is dominated 
by water-water interactions, driving the energy down.  Your mileage will vary 
depending on what you're dealing with.

> could you please help me out with this?

You need to parametrize the missing dihedral appropriately.  Placeholder values 
are as useful as deletion (they're not), so you need to invest time in building 
a sound force field model.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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