[gmx-users] KALP15 in DPPC

[negar habibzadeh]

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.


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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