[gmx-users] About BoxVector and APL

vidhya sankar scvsankar_agr at yahoo.com
Fri Nov 2 04:20:06 CET 2012

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
 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

Thanks In Advance

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