[gmx-users] KALP15 in DPPC

Mon Jan 29 15:11:44 CET 2018

On 1/28/18 3:22 PM, negar habibzadeh wrote:
> 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???

Water leaking in immediately at the end of equilibration is almost 
certainly spurious. Again, I suggest you build your system a different 
way or find a better method of equilibration. It shouldn't be hard to 
keep waters out if the system is built properly. If they then leak in 
over (long) simulations, it might be relevant.

-Justin

> 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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>> --
>> ==================================================
>>
>> 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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>> * Please search the archive at http://www.gromacs.org/Support
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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

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