[gmx-users] KALP15 in DPPC

Fri Feb 2 16:27:44 CET 2018

On 2/1/18 6:14 PM, negar habibzadeh wrote:
>   hi . I want to measure the distance between center of membrane and a
> peptide . how can i use gmx distance ??

What have you tried? Did it work or cause problems?

-Justin

> 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
>>>>>>>>>>
>>>>>>>>>> ==================================================
>>>>>>>>>>
>>>>>>>>>> --
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>>>>>>>>>> * Please search the archive at http://www.gromacs.org/Support
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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
>>>>>>>> /Mailing_Lists/GMX-Users_List before posting!
>>>>>>>>
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>>>>>>>>
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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
>>>>>> /Mailing_Lists/GMX-Users_List before posting!
>>>>>>
>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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>>>>>> 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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>>>>
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>>>> 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
>> /Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
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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

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