[gmx-users] KALP15 in DPPC

[Justin Lemkul]

On 1/25/18 12:17 PM, negar habibzadeh wrote:
> How much time is needed to run ? i changed from 100 ps ( restrained
> equilibration run ( nvt)) to 1 ns(1000ps) . but when i did npt (without
> water and lipids restraints) again i saw water inside membrane.

I don't know. Such protocols are usually not necessary for a properly 
prepared membrane. If you've got a huge amount of void space, I suggest 
trying a different method to build the system, because perhaps the 
starting coordinates are simply poor.

-Justin

>
> On Wed, Jan 24, 2018 at 10:51 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> 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
>>
>> ==================================================
>>
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>> Gromacs Users mailing list
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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

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