vinothkumar mohanakrishnan wrote:
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
Per your genbox command below, if you have one hexane (in hexane_box.gro) and
you add 200 (with -nmol), you should then have 201 hexane molecules in the system.
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.
Follow my previous advice and see if you can trace back where the error came
from. Count the molecules in your .gro file, i.e.:
grep OW hexane_solv.gro | wc -l
will give you the number of water molecules. Do something analogous for hexane.
You're off by 2820 atoms, which is in the ballpark of 940 waters, so something
has broken down pretty badly somewhere.
-Justin
; 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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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