i want to do MD for hexane-water system. I got hexane.gro and hexane..itp from PRODRG 2.5 Beta server with that i made the hexane.top file. below is the serious of commands i executed in gromacs, i am adding 200 hexane molecules an 1115 water molecules. after the first genbox i checked my topolgy file wheather the no .of hexane molecules got updated r increased to 200 but it doesn't and remains as 1 and then i maually changed it to 200 in the molecules section. i dont know where iam going wrong and i always get the error message as " number of coordinates in coordinate file (hexane_solv.gro, 7365) does not match topology (hexane.top, 4545) " while running grompp for energy minimisation. i read the error gromacs (website) documentation and found that the hexane.top r hexane.gro file is not getting updated, but iam helpless. any help is highly appreciated. below is my topology file as well.
; The force field files to be included #include "ffG43a1.itp" ; Include hexane topology #include "hexane.itp" ; Include SPC water topology #include "spc.itp" [ system ] hexane in Water [ molecules ] ;molecule name number hexane 200 SOL 1115 * Commands* editconf -f hexane.gro -o hexane_box.gro -c -bt triclinic -box 8.31 3.01 3.01 genbox -cp hexane_box.gro -ci hexane_box.gro -p hexane.top -o hexane_multi.gro -nmol 200 -seed 1997 genbox -cp hexane_multi.gro -cs spc216.gro -p hexane.top -o hexane_solv.gro grompp -f em.mdp -c hexane_solv.gro -p hexane.top -o hexane_em.tpr Regards Vinoth
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