[gmx-users] KALP15 in DPPC

Wed Jan 31 18:06:42 CET 2018

On 1/30/18 7:00 PM, negar habibzadeh wrote:
> hi. in my dopc.gro file i have 128 dopc ,5120 water (sol) with box size of
> 6.5   6.5   7.5 .i increase z direction from 7.5 nm  to 10 nm ,how can i
> add some extra water more than 5120 ??

Just run gmx solvate again.

-Justin

> On Mon, Jan 29, 2018 at 5:41 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> 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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>>>>>>>> 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
>>>>>>
>>>>>> * Please search the archive at http://www.gromacs.org/Support
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>>>>>>
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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
>>>>
>>>> * 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
>>
>> ==================================================
>>
>> --
>> Gromacs Users mailing list
>>
>> * 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

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