[gmx-users] KALP15 in DPPC

Justin Lemkul jalemkul at vt.edu
Wed Jan 24 13:55:08 CET 2018

On 1/24/18 5:02 AM, negar habibzadeh wrote:
> 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 ?

If there's lots of void space around the protein in the membrane, then 
you'll either need to prepare the system more carefully to prevent such 
voids, or do an equilibration with water molecules restrained in the 
z-dimension only, to prevent them from diffusing into the membrane. 
Then, remove the restraints and equilibrate again.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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