Dear Justin Thank you For your Previous Kind Reply I am following your Lipid-protein Tutorial for My system I Gave The Following Commands As Quoted in your Tutorial Also I Have Suitably Edited The Topology As in the Tutorial
Now the Problem in My solvation . I Gave The Following Commands As Quoted in your Tutorial ./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 I Repeated the inflate and EM Until I have Attained APL 66 (Experimental value 62) At the End of EMinimised .gro file The Box vectors Has been Increased form 6 6 6 6 to 20.57700 20.57700 6.00000 As result Box Size Also Increase When I solvate By mere Editing the Vanderwalls Radii to 0.470, then my system is is solvated By 64495 Water molecules How to Avoid this Problem ? This is too high Where I have Committed Mistakes I need your Valuable Ideas and Suggestions 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
