[gmx-users] KALP15 in DPPC

Wed Jan 31 01:00:05 CET 2018

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 ??

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
>>>>>>>
>>>>>>> ==================================================
>>>>>>>
>>>>>>> --
>>>>>>> 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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>>>>> * 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
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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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