Re: [gmx-users] genion: can you place the ions at one location in the box?

[Justin A. Lemkul]

Justin A. Lemkul wrote:



Smiruthi Ramasubramanian wrote:

Justin,

I tried to use an index file with atom numbers of the water molecules 
in the required volume.


But when I try to ionize the box, I get this error:
 
Fatal error:
The solvent group SOL is not continuous: index[717]=21689, 
index[718]=21696


This makes sense, but is there a way get around this?



The fundamental requirement of genion is that the solvent is continuous 
in the coordinate file.  If that's not true, genion won't work.  If you 
have continuous solvent, a valid index group within that section should 
work just fine.




Another option is to write your own script that replaces water molecules with 
the desired ion type; it should be relatively simple to randomly choose water 
molecules to replace based on simple coordinate criteria.  Updating the topology 
would have to be done manually, and you'd have to find a way to generate a 
syntactically correct coordinate file after making replacements, but that is 
also fairly simple I/O with, for example, Perl.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] genion: can you place the ions at one location in the box?

[Justin A. Lemkul]

Smiruthi Ramasubramanian wrote:

Justin,

I tried to use an index file with atom numbers of the water molecules in 
the required volume.


But when I try to ionize the box, I get this error:
 
Fatal error:

The solvent group SOL is not continuous: index[717]=21689, index[718]=21696

This makes sense, but is there a way get around this?



The fundamental requirement of genion is that the solvent is continuous in the 
coordinate file.  If that's not true, genion won't work.  If you have continuous 
solvent, a valid index group within that section should work just fine.


-Justin


SR

On Thu, Mar 25, 2010 at 5:17 PM, Justin A. Lemkul > wrote:




Smiruthi Ramasubramanian wrote:


I am simulating an ion channel and require help placing a
concentration of ions at one side of the box (below the membrane).


"Sidedness" is irrelevant in a periodic system; the water layers are
continuous with PBC.


SETUP: membrane + embedded protein in the center of the cube.

I tried to generate a smaller cube (of the required volume below
the cube), solvate, add ions and then /cat/ with the *.gro file
of my system before solvating. But when I solvate the system
with ions, the ions are removed.

Any suggestions as to how to handle this problem?


I don't fully understand what you tried to do, but it should be
possible to solvate the unit cell normally, create an index group
for the waters on one "side" of the membrane, and pass this index
file to the -n flag of genion. Creating the index file may involve
writing your own script to collect the atom numbers.  As far as I am
aware, make_ndx cannot, for example, select all water molecules
below/above some z-coordinate, which would be required for your
situation.

-Justin

-- 



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
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Re: [gmx-users] genion: can you place the ions at one location in the box?

[Smiruthi Ramasubramanian]

Justin,

I tried to use an index file with atom numbers of the water molecules in the
required volume.

But when I try to ionize the box, I get this error:

Fatal error:
The solvent group SOL is not continuous: index[717]=21689, index[718]=21696

This makes sense, but is there a way get around this?

SR

On Thu, Mar 25, 2010 at 5:17 PM, Justin A. Lemkul  wrote:

>
>
> Smiruthi Ramasubramanian wrote:
>
>>
>> I am simulating an ion channel and require help placing a concentration of
>> ions at one side of the box (below the membrane).
>>
>>
> "Sidedness" is irrelevant in a periodic system; the water layers are
> continuous with PBC.
>
>
>  SETUP: membrane + embedded protein in the center of the cube.
>>
>> I tried to generate a smaller cube (of the required volume below the
>> cube), solvate, add ions and then /cat/ with the *.gro file of my system
>> before solvating. But when I solvate the system with ions, the ions are
>> removed.
>>
>> Any suggestions as to how to handle this problem?
>>
>>
> I don't fully understand what you tried to do, but it should be possible to
> solvate the unit cell normally, create an index group for the waters on one
> "side" of the membrane, and pass this index file to the -n flag of genion.
> Creating the index file may involve writing your own script to collect the
> atom numbers.  As far as I am aware, make_ndx cannot, for example, select
> all water molecules below/above some z-coordinate, which would be required
> for your situation.
>
> -Justin
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-requ...@gromacs.org.
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>
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Re: [gmx-users] genion: can you place the ions at one location in the box?

[Justin A. Lemkul]

Smiruthi Ramasubramanian wrote:


I am simulating an ion channel and require help placing a concentration 
of ions at one side of the box (below the membrane).




"Sidedness" is irrelevant in a periodic system; the water layers are continuous 
with PBC.



SETUP: membrane + embedded protein in the center of the cube.

I tried to generate a smaller cube (of the required volume below the 
cube), solvate, add ions and then /cat/ with the *.gro file of my system 
before solvating. But when I solvate the system with ions, the ions are 
removed.


Any suggestions as to how to handle this problem?



I don't fully understand what you tried to do, but it should be possible to 
solvate the unit cell normally, create an index group for the waters on one 
"side" of the membrane, and pass this index file to the -n flag of genion. 
Creating the index file may involve writing your own script to collect the atom 
numbers.  As far as I am aware, make_ndx cannot, for example, select all water 
molecules below/above some z-coordinate, which would be required for your situation.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] genion: can you place the ions at one location in the box?

[Smiruthi Ramasubramanian]

I am simulating an ion channel and require help placing a concentration of
ions at one side of the box (below the membrane).

SETUP: membrane + embedded protein in the center of the cube.

I tried to generate a smaller cube (of the required volume below the cube),
solvate, add ions and then *cat* with the *.gro file of my system before
solvating. But when I solvate the system with ions, the ions are removed.

Any suggestions as to how to handle this problem?
-- 
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http://lists.gromacs.org/mailman/listinfo/gmx-users
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