[gmx-users] Maximum force on atom and unpacked lipids

[Justin Lemkul]

On 4/2/13 5:56 AM, sdshine wrote:
> Dear Users,
>
> I have inserted protein and carbohydrate in DPPC membrane according to the
> KALP
> tutorials. After inserting both molecules, I checked by using VMD, the atoms
> around my protein and ligand were overlapped. But I applied position
> restraints to protein and ligand and  run
> Inflategro scripts for shrinking and packing.
>
> Perl inflategro result
> ____________________
> There are 3 lipids within cut-off range...
> 1 will be removed from the upper leaflet...
> 2 will be removed from the lower leaflet...
> Writing scaled bilayer & centered protein...
>
> Calculating Area per lipid...
> Protein X-min/max: 11    47
> Protein Y-min/max: 19    45
> X-range: 36 A    Y-range: 26 A
> Building 36 X 26 2D grid on protein coordinates...
> Calculating area occupied by protein..
> full TMD..
> upper TMD....
> lower TMD....
> Area per protein: 7.5 nm^2
> Area per lipid: 10.4673818624 nm^2
>
> Area per protein, upper half: 5.5 nm^2
> Area per lipid, upper leaflet : 10.4160534349206 nm^2
>
> Area per protein, lower half: 4.25 nm^2
> Area per lipid, lower leaflet : 10.6042155870968 nm^2
>
> Writing Area per lipid...
> Done!
> ___________________
>
> 1st EM result
> _________
> ---
> -------
> Step=  576, Dmax= 8.0e-03 nm, Epot= -9.29249e+04 Fmax= 5.95606e+03, atom=
> 504
> Step=  578, Dmax= 4.8e-03 nm, Epot= -9.29638e+04 Fmax= 8.42117e+02, atom=
> 504
>
> writing lowest energy coordinates.
>
> Steepest Descents converged to Fmax < 1000 in 579 steps
> Potential Energy  = -9.2963797e+04
> Maximum force     =  8.4211664e+02 on atom 504
> Norm of force     =  4.9797871e+01
>
> Then in EM step, showing Maximum force on certain atom.
> I performed shrinking step until it converged. But every EM I have Max Force
> on selected atom.

There will always be some atom with a maximum force; that's how EM works.  As 
long as that maximum force is below an acceptable tolerance, there is no problem.

> The final complex still have unpacked lipids.

This statement doesn't make much sense to me.  Either InflateGRO worked, or it 
didn't.  There shouldn't be any halfway.

> How to correct this or whether will be corrected during Equilibration steps.
> I think the problem lies in the Ist EM step itself.
> Kindly give some suggestions
>

I don't see evidence of a problem, and certainly not within the first EM step.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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