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 <jalem...@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 <jalem...@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 <jalem...@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 <jalem...@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 <jalem...@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

jalem...@vt.edu | (540) 231-3129
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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

jalem...@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

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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

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send a mail to gmx-users-requ...@gromacs.org.


--
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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

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send a mail to gmx-users-requ...@gromacs.org.


--
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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

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send a mail to gmx-users-requ...@gromacs.org.


--
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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

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