[gmx-users] KALP15 in DPPC

Fri Feb 2 00:14:23 CET 2018

 hi . I want to measure the distance between center of membrane and a
peptide . how can i use gmx distance ??

On Wed, Jan 31, 2018 at 8:13 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>>>>>>>>>
>>>>>>>>> ==================================================
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> Gromacs Users mailing list
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>>>>>>>>> or
>>>>>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>>
>>>>>>>>> ==================================================
>>>>>>>>
>>>>>>> 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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>>>>>>> or
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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
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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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