[gmx-users] Maximum force on atom and unpacked lipids
jalemkul at vt.edu
Tue Apr 2 12:55:03 CEST 2013
On 4/2/13 5:56 AM, sdshine wrote:
> Dear Users,
> I have inserted protein and carbohydrate in DPPC membrane according to the
> 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...
> 1st EM result
> Step= 576, Dmax= 8.0e-03 nm, Epot= -9.29249e+04 Fmax= 5.95606e+03, atom=
> Step= 578, Dmax= 4.8e-03 nm, Epot= -9.29638e+04 Fmax= 8.42117e+02, atom=
> 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 A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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