[gmx-users] (no subject)

negar habibzadeh negarhze at gmail.com
Wed Jan 24 10:37:32 CET 2018

hi . i am doing simulation of peptide in DOPC bilayer. i have dopc.itp ,
dopc.pdb, dopc.gro , peptide.itp , sample.top for dopc ,
peptide.pdb,topol.top. i used below commands.

gmx editconf -f peptide.gro -o pep.gro -box 6.35172   6.80701   7.49241 -c
(it corresponds to the x/y/z box vectors of the DOPC unit cell)
i merg peptide and dopc:
cat pep.gro DOPC_323K.gro > tot1.gro
(I remove unnecessary lines)
i add ions :
gmx grompp -f ions.mdp -c tot1.gro -p mem.top -o ions.tpr
gmx genion -s ions.tpr -o tot.gro -p mem.top -pname NA -nname CL -nn 8
i get tpr file  (in mem.mdp i add some line to freeze protein )
gmx grompp -f mem.mdp -c tot.gro -p mem.top -o mem.tpr -n index.ndx
and i use g-membed command:
g_membed -f mem.tpr -dat mem.dat -c final.gro -n index.ndx -xyinit 0.1 (in
mem.dat i include the place of protein in the center of box)
in final.gro there were a few stray water molecules, i deleted them
manually and
i did energy minimization :
gmx grompp -f minim.mdp -c final.gro -p mem.top -o em.tpr
gmx mdrun -v -deffnm em
i checked em.gro , every thing is ok . but when i run nvt
in nvt.gro , A large number of water molecules are inside the membrane.
how can i solve this problem ?

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