[gmx-users] RE: Energy Minimization - not getting correct lipid area

Sat Jun 9 00:54:54 CEST 2012

How would I know what coordinate file to use? I have been following the tutorial word for word. However, I did not get the confout.gro file that I should have gotten after the minimization (mdrun -v -deffnm em) so I have been using em.gro. Would this be a problem?
________________________________
From: Justin A. Lemkul [via GROMACS] [ml-node+s5086n4998247h76 at n6.nabble.com]
Sent: Friday, June 08, 2012 5:42 PM
To: Hicks, Erica
Subject: RE: Energy Minimization - not getting correct lipid area

On 6/8/12 6:33 PM, Erica Hicks wrote:

> Hi,
>
> bash-3.2$ perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat
> Reading.....
> Scaling lipids....
> There are 128 lipids...
> with 50 atoms per lipid..
>
> Determining upper and lower leaflet...
> 64 lipids in the upper...
> 64 lipids in the lower leaflet
>
> Centering protein....
> Checking for overlap....
> ...this might actually take a while....
> 100 % done...
> There are 2 lipids within cut-off range...
> 1 will be removed from the upper leaflet...
> 1 will be removed from the lower leaflet...
>
> Writing scaled bilayer&  centered protein...
>
>
> Calculating Area per lipid...
> Protein X-min/max: 26    40
> Protein Y-min/max: 25    39
> X-range: 14 A    Y-range: 14 A
> Building 14 X 14 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: 10.4716089904762 nm^2
>
> Area per protein, upper half: 1.75 nm^2
> Area per lipid, upper leaflet : 10.4755772444444 nm^2
>
> Area per protein, lower half: 2 nm^2
> Area per lipid, lower leaflet : 10.4716089904762 nm^2
>
> Writing Area per lipid...
> Done!
>
> bash-3.2$ mdrun -v -deffnm em
> Back Off! I just backed up em.log to ./#em.log.6#
> Getting Loaded...
> Reading file em.tpr, VERSION 4.5.4 (single precision)
> Starting 4 threads
> Loaded with Money
>
> Making 1D domain decomposition 4 x 1 x 1
>
> Back Off! I just backed up em.trr to ./#em.trr.6#
>
> Back Off! I just backed up em.edr to ./#em.edr.6#
>
> Steepest Descents:
>     Tolerance (Fmax)   =  1.00000e+03
>     Number of steps    =        50000
> Step=    0, Dmax= 1.0e-02 nm, Epot= -3.06212e+05 Fmax= 5.37269e+03, atom= 3275
> Step=    1, Dmax= 1.0e-02 nm, Epot= -3.10498e+05 Fmax= 2.40668e+03, atom= 3024
> Step=    3, Dmax= 6.0e-03 nm, Epot= -3.10958e+05 Fmax= 2.89119e+03, atom= 4225
> Step=    5, Dmax= 3.6e-03 nm, Epot= -3.12589e+05 Fmax= 1.46767e+03, atom= 1365
> Step=    6, Dmax= 4.3e-03 nm, Epot= -3.13033e+05 Fmax= 3.83969e+03, atom= 1365
> Step=    7, Dmax= 5.2e-03 nm, Epot= -3.13599e+05 Fmax= 2.88720e+03, atom= 1365
> Step=    8, Dmax= 6.2e-03 nm, Epot= -3.13688e+05 Fmax= 4.93154e+03, atom= 1365
> Step=    9, Dmax= 7.5e-03 nm, Epot= -3.14101e+05 Fmax= 4.72541e+03, atom= 1365
> Step=   11, Dmax= 4.5e-03 nm, Epot= -3.14800e+05 Fmax= 9.90227e+02, atom= 1365
>
> writing lowest energy coordinates.
>
> Back Off! I just backed up em.gro to ./#em.gro.6#
>
> Steepest Descents converged to Fmax<  1000 in 12 steps
> Potential Energy  = -3.1480012e+05
> Maximum force     =  9.9022711e+02 on atom 1365
> Norm of force     =  1.2180042e+02
>
>
> bash-3.2$ perl inflategro.pl em.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat
> Reading.....
> Scaling lipids....
> There are 128 lipids...

Something is wrong here.  You should only have 126 lipids since 2 were removed
before.  Did you minimize the correct coordinate file?

> with 50 atoms per lipid..
>
> Determining upper and lower leaflet...
> 64 lipids in the upper...
> 64 lipids in the lower leaflet
>
> No protein coordinates found...

This is also strange.  This, coupled with the lines above regarding the number
of lipids, suggest you're using the wrong coordinate file.

> Writing scaled bilayer&  centered protein...
>
>
> Calculating Area per lipid...
> Protein X-min/max: 10000    -9999
> Protein Y-min/max: 10000    -9999
> X-range: -19999 A    Y-range: -19999 A
> Building -19999 X -19999 2D grid on protein coordinates...
> Calculating area occupied by protein..
> full TMD..
> upper TMD..
> lower TMD..

The following areas are meaningless, for reasons associated with incorrect
content or processing thereof.

> Area per protein: 0 nm^2
> Area per lipid: 0.583197761890625 nm^2
>
> Area per protein, upper half: 0 nm^2
> Area per lipid, upper leaflet : 0.583197761890625 nm^2
>
> Area per protein, lower half: 0 nm^2
> Area per lipid, lower leaflet : 0.583197761890625 nm^2
>
> Writing Area per lipid...
> Done!
>
> To me, it looks like it is not looking at the 126 lipids that I updated in the topology file. Hmmmm....

OK, I seem to remember 124 being what my system produced, but that's irrelevant.
  Check out the lines above.

> Erica
>
> ________________________________
> From: Justin A. Lemkul [via GROMACS] [[hidden email]<UrlBlockedError.aspx>]
> Sent: Friday, June 08, 2012 5:21 PM
> To: Hicks, Erica
> Subject: RE: Energy Minimization - not getting correct lipid area
>
>
>
> On 6/8/12 6:18 PM, Erica Hicks wrote:
>> Hi,
>>
>> Everything should be updated correctly. I added in the DPPC 128 underneath
>> the protein in [molecules] but I still get the same results. What do you mean
>> by " Further manual modifications are necessary based on how many lipids
>> InflateGRO removes"? After I generated the new position restrain file, I
>> updated the minim.mdp withe the correct info. I then scaled by a factor of 4,
>> updated [molecules], ran energy minimization (mdrun -v -deffnm em), and
>
> This is all my comment meant.  If InflateGRO removes 4 lipids, then you have 124
> left, which it sounds like you have accounted for.
>
>> scaled by a factor 0.95. I have no idea what could possibly going wrong.
>> Maybe something with the manipulation of InflateGRO????
>
> Please provide the entire screen output of the first shrinking step that
> InflateGRO produces.
>
> -Justin
>
> --
> ========================================
>
> 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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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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