[gmx-users] About BoxVector and APL

[Justin Lemkul]

On 11/1/12 11:20 PM, vidhya sankar wrote:
>
> As uou Told me in the Previous Mail I have Given My sereis of Commands With Real file Names
>
> ./pdb2gmx_d  -f 2KDQ.pdb -o 2KDQ.gro -ignh -ter -water spc
>   ./editconf_d  -f 2KDQ.gro -o 2KDQ_newbox.gro -box 6 6 6  -c
>   ./editconf_d -f dppc128.pdb -o dppc128n.gro -center 3 3 3  -box 6 6 6
>   ./grompp_d -f emdppc.mdp -c dppc128n.gro -p topol_dppc.top  -o emdppc.tpr -maxwarn 1
>   ./trjconv_d -s emdppc.tpr -f dppc128n.gro  -o dppc128_whole.gro  -pbc  mol -ur compact
>   ./editconf_d  -f 2KDQ.gro -o 2KDQ_newbox.gro -box 6 6 6  -c
>   cat 2KDQ_newbox.gro dppc128_whole.gro > system.gro
>   ./genrestr_d  -f 2KDQ_newbox.gro -o strong_posre.itp -fc 100000 100000 100000
>   perl inflategro.pl system.gro 4 DPPC 18 system_inflated.gro 5 area.dat
>   ./grompp_d -f emdppc.mdp -c system_inflated.gro -p 2KDQ.top  -o 2KDQDPPCem.tpr
>   ./mdrun_d  -v -deffnm 2KDQDPPCem
>   perl inflategro.pl 2KDQDPPCem.gro 0.95  DPPC 0 system_inflated1.gro 5 area1.dat
>   ./grompp_d -f emdppc.mdp -c system_inflated1.gro -p 2KDQ.top  -o 2KDQDPPCem1.tpr
>   ./mdrun_d  -v -deffnm 2KDQDPPCem1
> perl inflategro.pl 2KDQDPPCem1.gro 0.95  DPPC 0 system_inflated2.gro 5 area2.dat
>   ./grompp_d -f emdppc.mdp -c system_inflated2.gro -p 2KDQ.top  -o 2KDQDPPCem2.tpr
> ./mdrun_d  -v -deffnm 2KDQDPPCem2
>
> perl inflategro.pl 2KDQDPPCem2.gro 0.95  DPPC 0 system_inflated3.gro 5 area3.dat
> output for  My satisfactorily shrunken system  as follows
> Reading.....
>   Scaling lipids....
>   There are 127 lipids...
>   with 50 atoms per lipid..
>   Determining upper and lower leaflet...
>   64 lipids in the upper...
>   63 lipids in the lower leaflet
>   Centering protein....
>   Writing scaled bilayer & centered protein...
>   Calculating Area per lipid...
>   Protein X-min/max: 98    119
>   Protein Y-min/max: 99    117
>   X-range: 21 A    Y-range: 18 A
>   Building 21 X 18 2D grid on protein coordinates...
>   Calculating area occupied by protein..
>   full TMD..
>   upper TMD....
>   lower TMD....
>   Area per protein: 3.75 nm^2
>   Area per lipid: 6.60886502362205 nm^2
>   Area per protein, upper half: 2.75 nm^2
>   Area per lipid, upper leaflet : 6.572858265625 nm^2
>   Area per protein, lower half: 3 nm^2
>   Area per lipid, lower leaflet : 6.67322109523809 nm^2
>   Writing Area per lipid.
>
>   ./grompp_d -f emdppc.mdp -c system_inflated3.gro -p 2KDQ.top  -o 2KDQDPPCem3.tpr
> ./mdrun_d  -v -deffnm 2KDQDPPCem3
>
> In  the final Energy minimization  (2KDQDPPCem3.gro file) of the satisfactorily shrunken
> system  The Box vectors  Has been Increased form 6 6  6 6 to
>    20.57700  20.57700   6.00000
>
>   As you're suspecting I may be  confusing your files. In the beginning I am giving Series of Commands with Real files Name
>    Could you Please Suggests  Where i Have Confused in File Names ? Kindly Give me your Valuable Suggestion
>

Now it is clear to me that you're simply not done.  Three iterations of 
shrinking is not satisfactory.  6.57 nm^2 = 657 A^2.  Mind the square term in 
the conversion factor.  You have a long way to go yet.  Simple visualization of 
the system should have made this obvious.

-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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