[gmx-users] KALP15 in DPPC

negar habibzadeh negarhze at gmail.com
Wed Jan 24 17:16:07 CET 2018


i did it  but when i removed the restraints from water to equilibrate again
,(after new equilibration ) i saw some water molecules  inside the membrane
again. what can i do ?


On Wed, Jan 24, 2018 at 4:24 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ==================================================
>
> 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
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
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