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 Thanks In Advance -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists