Re: [gmx-users] KALP15 in DPPC

[Justin Lemkul]

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  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  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  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 
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 
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
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

* For (un)subscribe requests visit
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or
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) 

Re: [gmx-users] KALP15 in DPPC

[negar habibzadeh]

 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  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  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  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 
> 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 
>>> 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
>
> --
> ==

Re: [gmx-users] KALP15 in DPPC

[Justin Lemkul]

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  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  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  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 
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
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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
or
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

==

--
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 

Re: [gmx-users] KALP15 in DPPC

[negar habibzadeh]

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  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  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  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 
> 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
>>> 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!
>>>
>>> * 

Re: [gmx-users] KALP15 in DPPC

[Justin Lemkul]

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  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  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  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
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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
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

==

--
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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
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 

Re: [gmx-users] KALP15 in DPPC

[negar habibzadeh]

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???

On Thu, Jan 25, 2018 at 11:14 PM, Justin Lemkul  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  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  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
> 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
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> 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
>>>
>>> ==
>>>
>>> --
>>> 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
>>>
>>> * For (un)subscribe requests visit
>>> 

Re: [gmx-users] KALP15 in DPPC

[Justin Lemkul]

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  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  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
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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--
==

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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Re: [gmx-users] KALP15 in DPPC

[negar habibzadeh]

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.


On Wed, Jan 24, 2018 at 10:51 PM, Justin Lemkul  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  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
>>> 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
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> 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
>
> ==
>
> --
> 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
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] KALP15 in DPPC

[Justin Lemkul]

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

Re: [gmx-users] KALP15 in DPPC

[negar habibzadeh]

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 ?


On Wed, Jan 24, 2018 at 4:24 PM, Justin Lemkul  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
> 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
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
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Re: [gmx-users] KALP15 in DPPC

[Justin Lemkul]

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

Re: [gmx-users] KALP15 in DPPC

[negar habibzadeh]

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 ?

On Mon, Jan 22, 2018 at 4:19 PM, Justin Lemkul  wrote:

>
>
> On 1/21/18 1:23 PM, negar habibzadeh wrote:
>
>> hi . in vmd how can i find special number for each atom? i want to delete
>> those atoms from my gro file.
>>
>
> You can label atoms by clicking on them in label mode. If you have further
> questions about VMD, post to their mailing list.
>
> -Justin
>
>
> tnx
>>
>>
>> On Mon, Jan 15, 2018 at 9:12 PM, Justin Lemkul  wrote:
>>
>>
>>> On 1/15/18 10:56 AM, negar habibzadeh wrote:
>>>
>>> tnx so much
i got nvt.tpr and now i want to run it but i am getting this error :
 Fatal error:
 Too many LINCS warnings (5258)
 If you know what you are doing you can adjust the lincs warning
 threshold
 in your mdp file
 or set the environment variable GMX_MAXCONSTRWARN to -1,
 but normally it is better to fix the problem

 I use position restraints on the lipid headgroups for P of DOPC . i add
 the
 following lines to the system topology after the #include "dopc.itp"
 line.

 #include "DOPC.itp"

 #ifdef POSRES_LIPID
 #include "lipid_posre.itp"
 #endif

 and i add the following line in nvt.mdp :
 define  = -DPOSRES_protein  -DPOSRES_LIPID  ; Position restraint
 for each protein and for DOPC P

 i created lipid_posre.itp :

 ; position restraint file for DOPC P

 [ position_restraints ]
 ;  i funct   fcxfcyfcz
  201   0   0   1000
 ~

 i used position restraints for lipids but again when i want to run nvt
 ,i
 get this error :

 Fatal error:
 Too many LINCS warnings (5258)
 If you know what you are doing you can adjust the lincs warning
 threshold
 in your mdp file
 or set the environment variable GMX_MAXCONSTRWARN to -1,
 but normally it is better to fix the problem

 how can i solve this problem ?

 http://www.gromacs.org/Documentation/Terminology/Blowing_Up#
>>> Diagnosing_an_Unstable_System
>>>
>>> -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
>>> 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
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> 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
>
> ==
>
> --
> 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
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] KALP15 in DPPC

[Justin Lemkul]

On 1/21/18 1:23 PM, negar habibzadeh wrote:

hi . in vmd how can i find special number for each atom? i want to delete
those atoms from my gro file.


You can label atoms by clicking on them in label mode. If you have 
further questions about VMD, post to their mailing list.


-Justin


tnx


On Mon, Jan 15, 2018 at 9:12 PM, Justin Lemkul  wrote:



On 1/15/18 10:56 AM, negar habibzadeh wrote:


tnx so much
   i got nvt.tpr and now i want to run it but i am getting this error :
Fatal error:
Too many LINCS warnings (5258)
If you know what you are doing you can adjust the lincs warning threshold
in your mdp file
or set the environment variable GMX_MAXCONSTRWARN to -1,
but normally it is better to fix the problem

I use position restraints on the lipid headgroups for P of DOPC . i add
the
following lines to the system topology after the #include "dopc.itp" line.

#include "DOPC.itp"

#ifdef POSRES_LIPID
#include "lipid_posre.itp"
#endif

and i add the following line in nvt.mdp :
define  = -DPOSRES_protein  -DPOSRES_LIPID  ; Position restraint
for each protein and for DOPC P

i created lipid_posre.itp :

; position restraint file for DOPC P

[ position_restraints ]
;  i funct   fcxfcyfcz
 201   0   0   1000
~

i used position restraints for lipids but again when i want to run nvt  ,i
get this error :

Fatal error:
Too many LINCS warnings (5258)
If you know what you are doing you can adjust the lincs warning threshold
in your mdp file
or set the environment variable GMX_MAXCONSTRWARN to -1,
but normally it is better to fix the problem

how can i solve this problem ?


http://www.gromacs.org/Documentation/Terminology/Blowing_Up#
Diagnosing_an_Unstable_System

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

Re: [gmx-users] KALP15 in DPPC

[negar habibzadeh]

hi . in vmd how can i find special number for each atom? i want to delete
those atoms from my gro file.
tnx


On Mon, Jan 15, 2018 at 9:12 PM, Justin Lemkul  wrote:

>
>
> On 1/15/18 10:56 AM, negar habibzadeh wrote:
>
>> tnx so much
>>   i got nvt.tpr and now i want to run it but i am getting this error :
>> Fatal error:
>> Too many LINCS warnings (5258)
>> If you know what you are doing you can adjust the lincs warning threshold
>> in your mdp file
>> or set the environment variable GMX_MAXCONSTRWARN to -1,
>> but normally it is better to fix the problem
>>
>> I use position restraints on the lipid headgroups for P of DOPC . i add
>> the
>> following lines to the system topology after the #include "dopc.itp" line.
>>
>> #include "DOPC.itp"
>>
>> #ifdef POSRES_LIPID
>> #include "lipid_posre.itp"
>> #endif
>>
>> and i add the following line in nvt.mdp :
>> define  = -DPOSRES_protein  -DPOSRES_LIPID  ; Position restraint
>> for each protein and for DOPC P
>>
>> i created lipid_posre.itp :
>>
>> ; position restraint file for DOPC P
>>
>> [ position_restraints ]
>> ;  i funct   fcxfcyfcz
>> 201   0   0   1000
>> ~
>>
>> i used position restraints for lipids but again when i want to run nvt  ,i
>> get this error :
>>
>> Fatal error:
>> Too many LINCS warnings (5258)
>> If you know what you are doing you can adjust the lincs warning threshold
>> in your mdp file
>> or set the environment variable GMX_MAXCONSTRWARN to -1,
>> but normally it is better to fix the problem
>>
>> how can i solve this problem ?
>>
>
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up#
> Diagnosing_an_Unstable_System
>
> -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
> 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
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] KALP15 in DPPC

[Justin Lemkul]

On 1/15/18 10:56 AM, negar habibzadeh wrote:

tnx so much
  i got nvt.tpr and now i want to run it but i am getting this error :
Fatal error:
Too many LINCS warnings (5258)
If you know what you are doing you can adjust the lincs warning threshold
in your mdp file
or set the environment variable GMX_MAXCONSTRWARN to -1,
but normally it is better to fix the problem

I use position restraints on the lipid headgroups for P of DOPC . i add the
following lines to the system topology after the #include "dopc.itp" line.

#include "DOPC.itp"

#ifdef POSRES_LIPID
#include "lipid_posre.itp"
#endif

and i add the following line in nvt.mdp :
define  = -DPOSRES_protein  -DPOSRES_LIPID  ; Position restraint
for each protein and for DOPC P

i created lipid_posre.itp :

; position restraint file for DOPC P

[ position_restraints ]
;  i funct   fcxfcyfcz
201   0   0   1000
~

i used position restraints for lipids but again when i want to run nvt  ,i
get this error :

Fatal error:
Too many LINCS warnings (5258)
If you know what you are doing you can adjust the lincs warning threshold
in your mdp file
or set the environment variable GMX_MAXCONSTRWARN to -1,
but normally it is better to fix the problem

how can i solve this problem ?


http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System

-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
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

* For (un)subscribe requests visit
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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] KALP15 in DPPC

[negar habibzadeh]

tnx so much
 i got nvt.tpr and now i want to run it but i am getting this error :
Fatal error:
Too many LINCS warnings (5258)
If you know what you are doing you can adjust the lincs warning threshold
in your mdp file
or set the environment variable GMX_MAXCONSTRWARN to -1,
but normally it is better to fix the problem

I use position restraints on the lipid headgroups for P of DOPC . i add the
following lines to the system topology after the #include "dopc.itp" line.

#include "DOPC.itp"

#ifdef POSRES_LIPID
#include "lipid_posre.itp"
#endif

and i add the following line in nvt.mdp :
define  = -DPOSRES_protein  -DPOSRES_LIPID  ; Position restraint
for each protein and for DOPC P

i created lipid_posre.itp :

; position restraint file for DOPC P

[ position_restraints ]
;  i funct   fcxfcyfcz
   201   0   0   1000
~

i used position restraints for lipids but again when i want to run nvt  ,i
get this error :

Fatal error:
Too many LINCS warnings (5258)
If you know what you are doing you can adjust the lincs warning threshold
in your mdp file
or set the environment variable GMX_MAXCONSTRWARN to -1,
but normally it is better to fix the problem

how can i solve this problem ?




On Mon, Jan 15, 2018 at 6:29 PM, Justin Lemkul  wrote:

>
>
> On 1/15/18 6:18 AM, negar habibzadeh wrote:
>
>> tnx Justin .
>> now I am doing  Simulation of *5 *Peptide in DOPC Lipids  I am following
>>
>> your tutorial, in NVT equilibration step I created index file , with
>> program make_ndx (gmx make_ndx -f em.gro -o index.ndx) :
>>0 System  : 30700 atoms
>>1 Other   : 18744 atoms
>>2 FR1 :   160 atoms
>>3 FR2 :   220 atoms
>>4 FR3 :   240 atoms
>>5 FR4 :   205 atoms
>>6 FR5 :   255 atoms
>>7 DOPC: 17664 atoms
>>8 CL  :40 atoms
>>9 Water   : 11916 atoms
>>   10 SOL : 11916 atoms
>>   11 non-Water   : 18784 atoms
>>   12 Ion :40 atoms
>>   13 FR1 :   160 atoms
>>   14 FR2 :   220 atoms
>>   15 FR3 :   240 atoms
>>   16 FR4 :   205 atoms
>>   17 FR5 :   255 atoms
>>   18 DOPC: 17664 atoms
>>   19 CL  :40 atoms
>>   20 Water_and_ions  : 11956 atoms
>>
>>   nr : group   !   'name' nr name   'splitch' nrEnter: list groups
>>   'a': atom&   'del' nr 'splitres' nr   'l': list residues
>>   't': atom type   |   'keep' nr'splitat' nr'h': help
>>   'r': residue 'res' nr 'chain' char
>>   "name": group'case': case sensitive   'q': save and quit
>>   'ri': residue index
>>
>> 2|3|4|5|6
>>>
>> Copied index group 2 'FR1'
>> Copied index group 3 'FR2'
>> Merged two groups with OR: 160 220 -> 380
>> Copied index group 4 'FR3'
>> Merged two groups with OR: 380 240 -> 620
>> Copied index group 5 'FR4'
>> Merged two groups with OR: 620 205 -> 825
>> Copied index group 6 'FR5'
>> Merged two groups with OR: 825 255 -> 1080
>>
>>   21 FR1_FR2_FR3_FR4_FR5 :  1080 atoms
>>
>> name 21 protein
>>>
>>
>> 21|7
>>>
>> Copied index group 21 'protein'
>> Copied index group 7 'DOPC'
>> Merged two groups with OR: 1080 17664 -> 18744
>>
>>   22 protein_DOPC: 18744 atoms
>>
>> 10|8
>>>
>> Copied index group 10 'SOL'
>> Copied index group 8 'CL'
>> Merged two groups with OR: 11916 40 -> 11956
>>
>>   23 SOL_CL  : 11956 atoms
>>
>> q
>>>
>> then ... when i run grommp (gmx grompp -f nvt.mdp -c em.gro -p topol.top
>> -n
>> index.ndx -o nvt.tpr)  I'm getting this error:
>> Fatal error:
>> Group D0PC referenced in the .mdp file was not found in the index file.
>> Group names must match either [moleculetype] names or custom index group
>> names, in which case you must supply an index file to the '-n' option
>> of grompp.
>>
>> my nvt.mdp file is that
>>
>> Can anyone help me with the following fault in Gromacs during the NVT
>> equilibrium?
>>
>
> The error specifies that you've got "D0PC" instead of "DOPC" somewhere in
> the .mdp file (note zero instead of the letter O).
>
> -Justin
>
>
>
>> On Tue, Jan 9, 2018 at 4:31 PM, Justin Lemkul  wrote:
>>
>>
>>> On 1/7/18 3:07 AM, negar habibzadeh wrote:
>>>
>>> I am doing  Simulation of *γ-AA*Peptide in DOPC Lipids  I am following
 your tutorial  When I use inflategro script For my System I have got
 Output System_inflated.gro file with certain message in Command prompt
 as follows  . The Below Message Shows That There is No Lipid Molecules
 Are Deleted  Should I Change the Cut-off or scaling Factor  to Delete
 the Lipid Molecules or is it enough ,  I Mean  Must Some Lipid
 Molecules Need to be Deleted ?

 Maybe there just aren't any lipids overlapping with the protein; that
>>> can
>>> 

Re: [gmx-users] KALP15 in DPPC

[Justin Lemkul]

On 1/15/18 6:18 AM, negar habibzadeh wrote:

tnx Justin .
now I am doing  Simulation of *5 *Peptide in DOPC Lipids  I am following
your tutorial, in NVT equilibration step I created index file , with
program make_ndx (gmx make_ndx -f em.gro -o index.ndx) :
   0 System  : 30700 atoms
   1 Other   : 18744 atoms
   2 FR1 :   160 atoms
   3 FR2 :   220 atoms
   4 FR3 :   240 atoms
   5 FR4 :   205 atoms
   6 FR5 :   255 atoms
   7 DOPC: 17664 atoms
   8 CL  :40 atoms
   9 Water   : 11916 atoms
  10 SOL : 11916 atoms
  11 non-Water   : 18784 atoms
  12 Ion :40 atoms
  13 FR1 :   160 atoms
  14 FR2 :   220 atoms
  15 FR3 :   240 atoms
  16 FR4 :   205 atoms
  17 FR5 :   255 atoms
  18 DOPC: 17664 atoms
  19 CL  :40 atoms
  20 Water_and_ions  : 11956 atoms

  nr : group   !   'name' nr name   'splitch' nrEnter: list groups
  'a': atom&   'del' nr 'splitres' nr   'l': list residues
  't': atom type   |   'keep' nr'splitat' nr'h': help
  'r': residue 'res' nr 'chain' char
  "name": group'case': case sensitive   'q': save and quit
  'ri': residue index


2|3|4|5|6

Copied index group 2 'FR1'
Copied index group 3 'FR2'
Merged two groups with OR: 160 220 -> 380
Copied index group 4 'FR3'
Merged two groups with OR: 380 240 -> 620
Copied index group 5 'FR4'
Merged two groups with OR: 620 205 -> 825
Copied index group 6 'FR5'
Merged two groups with OR: 825 255 -> 1080

  21 FR1_FR2_FR3_FR4_FR5 :  1080 atoms


name 21 protein



21|7

Copied index group 21 'protein'
Copied index group 7 'DOPC'
Merged two groups with OR: 1080 17664 -> 18744

  22 protein_DOPC: 18744 atoms


10|8

Copied index group 10 'SOL'
Copied index group 8 'CL'
Merged two groups with OR: 11916 40 -> 11956

  23 SOL_CL  : 11956 atoms


q

then ... when i run grommp (gmx grompp -f nvt.mdp -c em.gro -p topol.top -n
index.ndx -o nvt.tpr)  I'm getting this error:
Fatal error:
Group D0PC referenced in the .mdp file was not found in the index file.
Group names must match either [moleculetype] names or custom index group
names, in which case you must supply an index file to the '-n' option
of grompp.

my nvt.mdp file is that

Can anyone help me with the following fault in Gromacs during the NVT
equilibrium?


The error specifies that you've got "D0PC" instead of "DOPC" somewhere 
in the .mdp file (note zero instead of the letter O).


-Justin



On Tue, Jan 9, 2018 at 4:31 PM, Justin Lemkul  wrote:



On 1/7/18 3:07 AM, negar habibzadeh wrote:


I am doing  Simulation of *γ-AA*Peptide in DOPC Lipids  I am following
your tutorial  When I use inflategro script For my System I have got
Output System_inflated.gro file with certain message in Command prompt
as follows  . The Below Message Shows That There is No Lipid Molecules
Are Deleted  Should I Change the Cut-off or scaling Factor  to Delete
the Lipid Molecules or is it enough ,  I Mean  Must Some Lipid
Molecules Need to be Deleted ?


Maybe there just aren't any lipids overlapping with the protein; that can
happen.

-Justin


There are 128 lipids...

with 138 atoms per lipid..

Determining upper and lower leaflet...
64 lipids in the upper...
64 lipids in the lower leaflet

Centering protein
Checking for overlap
...this might actually take a while
100 % done...
There are 0 lipids within cut-off range...
0 will be removed from the upper leaflet...
0 will be removed from the lower leaflet...

Writing scaled bilayer & centered protein...


Calculating Area per lipid...
Protein X-min/max: 2441
Protein Y-min/max: 2343
X-range: 17 AY-range: 20 A
Building 17 X 20 2D grid on protein coordinates...
Calculating area occupied by protein..
full TMD..
upper TMD
lower TMD
Area per protein: 3.25 nm^2
Area per lipid: 10.7582741393 nm^2

Area per protein, upper half: 2.25 nm^2
Area per lipid, upper leaflet : 10.7738991393 nm^2

Area per protein, lower half: 2.5 nm^2
Area per lipid, lower leaflet : 10.7699928893 nm^2

Writing Area per lipid...
Done!


--
==

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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Re: [gmx-users] KALP15 in DPPC

[negar habibzadeh]

tnx Justin .
now I am doing  Simulation of *5 *Peptide in DOPC Lipids  I am following
your tutorial, in NVT equilibration step I created index file , with
program make_ndx (gmx make_ndx -f em.gro -o index.ndx) :
  0 System  : 30700 atoms
  1 Other   : 18744 atoms
  2 FR1 :   160 atoms
  3 FR2 :   220 atoms
  4 FR3 :   240 atoms
  5 FR4 :   205 atoms
  6 FR5 :   255 atoms
  7 DOPC: 17664 atoms
  8 CL  :40 atoms
  9 Water   : 11916 atoms
 10 SOL : 11916 atoms
 11 non-Water   : 18784 atoms
 12 Ion :40 atoms
 13 FR1 :   160 atoms
 14 FR2 :   220 atoms
 15 FR3 :   240 atoms
 16 FR4 :   205 atoms
 17 FR5 :   255 atoms
 18 DOPC: 17664 atoms
 19 CL  :40 atoms
 20 Water_and_ions  : 11956 atoms

 nr : group   !   'name' nr name   'splitch' nrEnter: list groups
 'a': atom&   'del' nr 'splitres' nr   'l': list residues
 't': atom type   |   'keep' nr'splitat' nr'h': help
 'r': residue 'res' nr 'chain' char
 "name": group'case': case sensitive   'q': save and quit
 'ri': residue index

> 2|3|4|5|6

Copied index group 2 'FR1'
Copied index group 3 'FR2'
Merged two groups with OR: 160 220 -> 380
Copied index group 4 'FR3'
Merged two groups with OR: 380 240 -> 620
Copied index group 5 'FR4'
Merged two groups with OR: 620 205 -> 825
Copied index group 6 'FR5'
Merged two groups with OR: 825 255 -> 1080

 21 FR1_FR2_FR3_FR4_FR5 :  1080 atoms

> name 21 protein


> 21|7

Copied index group 21 'protein'
Copied index group 7 'DOPC'
Merged two groups with OR: 1080 17664 -> 18744

 22 protein_DOPC: 18744 atoms

> 10|8

Copied index group 10 'SOL'
Copied index group 8 'CL'
Merged two groups with OR: 11916 40 -> 11956

 23 SOL_CL  : 11956 atoms

> q

then ... when i run grommp (gmx grompp -f nvt.mdp -c em.gro -p topol.top -n
index.ndx -o nvt.tpr)  I'm getting this error:
Fatal error:
Group D0PC referenced in the .mdp file was not found in the index file.
Group names must match either [moleculetype] names or custom index group
names, in which case you must supply an index file to the '-n' option
of grompp.

my nvt.mdp file is that

Can anyone help me with the following fault in Gromacs during the NVT
equilibrium?


On Tue, Jan 9, 2018 at 4:31 PM, Justin Lemkul  wrote:

>
>
> On 1/7/18 3:07 AM, negar habibzadeh wrote:
>
>> I am doing  Simulation of *γ-AA*Peptide in DOPC Lipids  I am following
>> your tutorial  When I use inflategro script For my System I have got
>> Output System_inflated.gro file with certain message in Command prompt
>> as follows  . The Below Message Shows That There is No Lipid Molecules
>> Are Deleted  Should I Change the Cut-off or scaling Factor  to Delete
>> the Lipid Molecules or is it enough ,  I Mean  Must Some Lipid
>> Molecules Need to be Deleted ?
>>
>
> Maybe there just aren't any lipids overlapping with the protein; that can
> happen.
>
> -Justin
>
>
> There are 128 lipids...
>> with 138 atoms per lipid..
>>
>> Determining upper and lower leaflet...
>> 64 lipids in the upper...
>> 64 lipids in the lower leaflet
>>
>> Centering protein
>> Checking for overlap
>> ...this might actually take a while
>> 100 % done...
>> There are 0 lipids within cut-off range...
>> 0 will be removed from the upper leaflet...
>> 0 will be removed from the lower leaflet...
>>
>> Writing scaled bilayer & centered protein...
>>
>>
>> Calculating Area per lipid...
>> Protein X-min/max: 2441
>> Protein Y-min/max: 2343
>> X-range: 17 AY-range: 20 A
>> Building 17 X 20 2D grid on protein coordinates...
>> Calculating area occupied by protein..
>> full TMD..
>> upper TMD
>> lower TMD
>> Area per protein: 3.25 nm^2
>> Area per lipid: 10.7582741393 nm^2
>>
>> Area per protein, upper half: 2.25 nm^2
>> Area per lipid, upper leaflet : 10.7738991393 nm^2
>>
>> Area per protein, lower half: 2.5 nm^2
>> Area per lipid, lower leaflet : 10.7699928893 nm^2
>>
>> Writing Area per lipid...
>> Done!
>>
>
> --
> ==
>
> 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
>
> ==
>
> --
> Gromacs Users mailing list
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> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
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> send a 

Re: [gmx-users] KALP15 in DPPC

[Justin Lemkul]

On 1/7/18 3:07 AM, negar habibzadeh wrote:

I am doing  Simulation of *γ-AA*Peptide in DOPC Lipids  I am following
your tutorial  When I use inflategro script For my System I have got
Output System_inflated.gro file with certain message in Command prompt
as follows  . The Below Message Shows That There is No Lipid Molecules
Are Deleted  Should I Change the Cut-off or scaling Factor  to Delete
the Lipid Molecules or is it enough ,  I Mean  Must Some Lipid
Molecules Need to be Deleted ?


Maybe there just aren't any lipids overlapping with the protein; that 
can happen.


-Justin


There are 128 lipids...
with 138 atoms per lipid..

Determining upper and lower leaflet...
64 lipids in the upper...
64 lipids in the lower leaflet

Centering protein
Checking for overlap
...this might actually take a while
100 % done...
There are 0 lipids within cut-off range...
0 will be removed from the upper leaflet...
0 will be removed from the lower leaflet...

Writing scaled bilayer & centered protein...


Calculating Area per lipid...
Protein X-min/max: 2441
Protein Y-min/max: 2343
X-range: 17 AY-range: 20 A
Building 17 X 20 2D grid on protein coordinates...
Calculating area occupied by protein..
full TMD..
upper TMD
lower TMD
Area per protein: 3.25 nm^2
Area per lipid: 10.7582741393 nm^2

Area per protein, upper half: 2.25 nm^2
Area per lipid, upper leaflet : 10.7738991393 nm^2

Area per protein, lower half: 2.5 nm^2
Area per lipid, lower leaflet : 10.7699928893 nm^2

Writing Area per lipid...
Done!


--
==

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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Re: [gmx-users] KALP15 in DPPC: Bilayer out of solvation box

[Justin Lemkul]

On 1/1/18 10:01 PM, Seketoulie Keretsu wrote:

Dear Experts

I am currently doing the gromacs tutorial for simulation of membrane
protein (KALP15 in DPPC by Justin A. Lemkul). I came across several
challenges most of which I could resolve. However, the result after
solvation wasn't as expected. That is, a small portion of the DPPC
bilayer was out of the solvation box and also the the water was no
distributed over the system as mentioned in tutorial (or atleast it
wasn't observable in VMD). I have done just as in the tutorial. I have
no clue why the bilayer went outside the solvation box since i
followed and executed just as mentioned in the tutorial. I suspect the
later issue, that is, the distribution of water all over the system
could be due to the step in which the changing of the value of C from
0.15 to 0.375 in vdwradii.dat wasn't effective.


I see from your RG post 
(https://www.researchgate.net/post/Gromacs_tutorial_preparation_and_simulation_of_a_simple_membrane_protein_available) 
that you are solvating during the InflateGRO steps. The tutorial does 
not tell you to do that, so don't. All of those minimizations should be 
carried out in vacuo.



My questions are:

1. Are the other membrane protein simulation tutorials available.
Perhaps more comprehensive ones?


What would you define as "more comprehensive" that would be more useful?

Note that my tutorial warns that it is advanced and users are expected 
to understand lots of routine things that I don't explicitly say in the 
tutorial. If there are elements that are unclear, then I'm happy to hear 
about them. It's been online for about 9 years now, and my email has 
significantly tapered off, so I'm assuming most issues have been 
resolved over time, but if that's not the case, feedback is always welcome.



2. After changing the value of C to 0.375 in the vdwradii.dat file at
the working directory, should i copy the vdwradii.dat to
/home//gromacs/top directory (where the file was originally
located)?


No, because then your increased C radius is globally applied to every 
system you work with, which won't be appropriate.


-Justin

3. The tutorial mentioned " Placing the new gromos53a6_lipid.ff
directory in $GMXLIB will allow you to use this force field
system-wide." I am unable to locate 'GMXLIB'. Does GMXLIB refer to the
directory in which the forcefield files (eg. ffnonbonded.ipt) were
located or should i create a GMXLIB directory.

The problems seems trivial however I am unable to proceed beyond
solvation. Kindly give suggestions.

  Thank you.


Sincerely,
Seke


--
==

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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Re: [gmx-users] KALP15 in DPPC: Bilayer out of solvation box

[Mark Abraham]

Hi,

On Tue, Jan 2, 2018 at 3:02 AM Seketoulie Keretsu 
wrote:

> Dear Experts
>
> I am currently doing the gromacs tutorial for simulation of membrane
> protein (KALP15 in DPPC by Justin A. Lemkul). I came across several
> challenges most of which I could resolve. However, the result after
> solvation wasn't as expected. That is, a small portion of the DPPC
> bilayer was out of the solvation box and also the the water was no
> distributed over the system as mentioned in tutorial (or atleast it
> wasn't observable in VMD). I have done just as in the tutorial. I have
> no clue why the bilayer went outside the solvation box since i
> followed and executed just as mentioned in the tutorial.


This just seems like normal consequences of a simulation using periodic
boundary conditions that are then visualized without considering those
consequences... see
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions


> I suspect the
> later issue, that is, the distribution of water all over the system
> could be due to the step in which the changing of the value of C from
> 0.15 to 0.375 in vdwradii.dat wasn't effective.
>

Why do you think that? Did you compare with leaving the value unmodified?


> My questions are:
>
> 1. Are the other membrane protein simulation tutorials available.
> Perhaps more comprehensive ones?
>

Justin's tutorials are of very high quality and rather comprehensive.


> 2. After changing the value of C to 0.375 in the vdwradii.dat file at
> the working directory, should i copy the vdwradii.dat to
> /home//gromacs/top directory (where the file was originally
> located)?
>

You should do whatever the tutorial suggests. In practice, both work the
same. Being able to leave the modified file in the working directory is
convenient in multiple ways.


> 3. The tutorial mentioned " Placing the new gromos53a6_lipid.ff
> directory in $GMXLIB will allow you to use this force field
> system-wide." I am unable to locate 'GMXLIB'. Does GMXLIB refer to the
> directory in which the forcefield files (eg. ffnonbonded.ipt) were
> located or should i create a GMXLIB directory.
>

GMXLIB is an environment variable that is set up when you run "source
/path/to/GMXRC" that helps the tools find the databases in
/path/to/gromacs/share/top. You could put the directory there, or leave it
in your working directory, whatever is more useful and convenient for you.
Do you plan to use it again?

Mark


> The problems seems trivial however I am unable to proceed beyond
> solvation. Kindly give suggestions.
>
>  Thank you.
>
>
> Sincerely,
> Seke
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Re: [gmx-users] KALP15 in DPPC Analysis section

[Justin Lemkul]

On 10/27/16 2:18 PM, Sailesh Bataju wrote:

Hi,

I've been following KAlP15 in DPPC tutorial successfully but now I stuck in
the last Analysis section. I googled the problem there's nothing out. The
question is so simple it's just a misunderstanding. In the 2nd part Density
of the Membrane the code is

# gmx make_ndx -f md_0_1.tpr -o density_groups.ndx
...
 > 12 & a C1 | a C2 | a C3 | a N4 | ... | a O11
 > name 22 Headgroups
 > 12 & a C12 | a C13 | a O14 | ... | a C50
 > name 23 Tails
 > q

I don't get what should I've to put in place of "..." . It's so confusing.
In 1st line after aN4, should I continue from "a N5 to a N10" or  "a O0 to
a O10"?

Similarly, in 3rd line after a O14, should I continue from "a O15 to a O49"
or "a C15 to a C49"?

Or, N and O are just typo, instead C should be placed?



The atom names are right.  Look at the coordinate file, and label the atoms 
using visualization software if you need to.  It's pretty standard lipid 
nomenclature.


The ellipsis (...) means "I've already typed up this whole tutorial and now I'm 
tired of typing all of this, so you fill in the blank here with the necessary 
atom names."  This implies that you have already familiarized yourself with what 
atom names constitute the lipid headgroup (note that I've stopped at O11, which 
means that's the end of the headgroup) and the tails (which start from C12).


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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