[gmx-users] EM in kalp15_DPPC

[Justin Lemkul]

On 8/21/12 6:14 AM, Shima Arasteh wrote:
>
>
>
> Hi,
>
> I'm doing the KALP-15 IN DPPC through the Justin's tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html
> The problem I got stuck into, is in "2. Pack the lipids around the protein" step.
> After generating the new position restrain file, I start to energy minimization to get the correct area per lipid. As below:
>
>   Scale the lipid positions by a factor of 4:
>       #perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat
>
>   LOOP :
>      "
>       Energy minimization with restrained protein
>       #grompp -f minim.mdp -c system_inflated.gro -p topol.top -o em.tpr -maxwarn 1

Why are you using -maxwarn?  It's almost always a bad idea.  What error are you 
trying to circumvent?

>       #mdrun -deffnm em
>       scale down the lipids by a factor of 0.95
>       #perl inflategro.pl em.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat
>      "
>
>
> The EM contains a warning:
>     Tolerance (Fmax)   =  1.00000e+03
>     Number of steps    =        50000
> Warning: 1-4 interaction between 2321 and 2325 at distance 2.307 which is larger than the 1-4 table size 2.200 nm
> These are ignored for the rest of the simulation
> This usually means your system is exploding,
> if not, you should increase table-extension in your mdp file
> or with user tables increase the table size
>
> but because of the -maxwarn 1 its output is:
>
> Steepest Descents converged to Fmax < 1000 in 557 steps
> Potential Energy  = -9.2383398e+04
> Maximum force     =  9.0041455e+02 on atom 65
> Norm of force     =  7.1919853e+01
>
> First, is it acceptable to ignore that warning?
>

Generally not.  You should check your input and output configurations carefully. 
  Something is wrong.

> # perl inflategro.pl em.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat
> Determining upper and lower leaflet...
> 66 lipids in the upper...
> 62 lipids in the lower leaflet
>
> Centering protein....
> Writing scaled bilayer & centered protein...
>
>
> Calculating Area per lipid...
> Protein X-min/max: 122    136
> Protein Y-min/max: 122    135
> X-range: 14 A    Y-range: 13 A
> Building 14 X 13 2D grid on protein coordinates...
> Calculating area occupied by protein..
> full TMD..
> upper TMD....
> lower TMD....
> Area per protein: 2 nm^2
> Area per lipid: 9.29991419025 nm^2
>
> Area per protein, upper half: 1.75 nm^2
> Area per lipid, upper leaflet : 9.02188648751515 nm^2
>
> Area per protein, lower half: 2 nm^2
> Area per lipid, lower leaflet : 9.59991142219355 nm^2
>
> Writing Area per lipid...
> Done!
>
> Here, the area per lipid is too far from 71 Å2!
>

Then you haven't done enough iterations of shrinking.  The outcome from 26 
iterations of shrinking is very reproducible.

-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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