[gmx-users] KALP15 in DPPC

[Justin Lemkul]

On 1/24/18 11:16 AM, negar habibzadeh wrote:
> 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 ?

Let the restrained equilibration run longer. Make sure you're not 
restraining the lipids in any way.

-Justin

>
> 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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-- 
==================================================

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

==================================================