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.<br><br>; The force field files to be included<br>#include "ffG43a1.itp"<br><br>; Include hexane topology<br>#include "hexane.itp"<br>
<br>; Include SPC water topology<br>#include "spc.itp"<br><br>[ system ]<br>hexane in Water<br><br>[ molecules ]<br>;molecule name number<br>hexane 200<br>SOL 1115<br><b><br>Commands</b><br>
<br> editconf -f hexane.gro -o hexane_box.gro -c -bt triclinic -box 8.31 3.01 3.01<br><br>genbox -cp hexane_box.gro -ci hexane_box.gro -p hexane.top -o hexane_multi.gro -nmol 200 -seed 1997<br><br>genbox -cp hexane_multi.gro -cs spc216.gro -p hexane.top -o hexane_solv.gro<br>
<br>grompp -f em.mdp -c hexane_solv.gro -p hexane.top -o hexane_em.tpr<br><br>Regards<br>Vinoth<br>