[gmx-users] KALP15 in DPPC

[negar habibzadeh]

my peptide is a cpp (cell penetrating peptide) . i am going to simulation
this peptide in dopc bilayer , i did lots of methods to build the system
but in nvt step i saw water inside dopc (i used posre for water but when i
removed it to run npt or md ,my problem was not solved ).Is it true that my
peptide causes water to enter into the membrane because it is a cpp???

On Thu, Jan 25, 2018 at 11:14 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> ==================================================
>
> --
> Gromacs Users mailing list
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