Re: [gmx-users] Index file

[Shima Arasteh]

I used genconf and got a new gro file. Then I saw the ions are not recognized 
because of the same numbering of ions with last SOL molecules. Therefore, I 
changed them manually, so the problem was solved.
Thanks for your suggestions dear Justin. 
Happy New Year! 
 

Sincerely,
Shima


- Original Message -
From: Justin Lemkul 
To: Shima Arasteh 
Cc: 
Sent: Monday, December 31, 2012 8:37 PM
Subject: Re: [gmx-users] Index file



On 12/31/12 11:58 AM, Shima Arasteh wrote:
> These are the last line of my gro file:
>
>      5SOL    HW299818   7.429   8.372  11.524
>      5CL      CL99819   0.485   3.864  11.451
>      5CL      CL99820   5.689   6.730   9.692
>     9.21490   8.92980  12.40750
>
>
> Here, I brought you the output of make_ndx command. As you see CL ions are 
> not recognized here.
>
>   Analysing residue names:
> There are:    48    Protein residues
> There are:   238      Other residues
> There are: 12624      Water residues
> Analysing Protein...
> Analysing residues not classified as Protein/DNA/RNA/Water and splitting into 
> groups...
>
>    0 System              : 99817 atoms
>    1 Protein             :   720 atoms
>    2 Protein-H           :   356 atoms
>    3 C-alpha             :    48 atoms
>    4 Backbone            :   144 atoms
>    5 MainChain           :   190 atoms
>    6 MainChain+Cb        :   234 atoms
>    7 MainChain+H         :   240 atoms
>    8 SideChain           :   480 atoms
>    9 SideChain-H         :   166 atoms
>   10 Prot-Masses         :   720 atoms
>   11 non-Protein         : 99097 atoms
>   12 Other               : 31892 atoms
>   13 POPC                : 31892 atoms
>   14 Water               : 67205 atoms
>   15 SOL                 : 67205 atoms
>   16 non-Water           : 32612 atoms
>
>   nr : group       !   'name' nr name   'splitch' nr    Enter: 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
>
>
> Somehow confusing for me!
>

It could be that both your last SOL and both CL ions have the same residue 
number.  Renumber the file with genconf and try again.  The only other thing I 
can think of is that you don't have an entry for CL in residuetypes.dat 
indicating that it is an ion.  The "Ion" group should be generated by default 
whenever an ion is encountered, but you don't have one.

-Justin

-- 


Justin A. Lemkul, Ph.D.
Research Scientist
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] Index file

[Luis Felipe Pineda de Castro]

A good minded advice Shima: think more for your self; science is not easy, or 
if it's not possible, ask ur adviser, or look for a new job.


From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf 
Of Shima Arasteh [shima_arasteh2...@yahoo.com]
Sent: Monday, December 31, 2012 5:58 PM
To: Justin Lemkul; Discussion list for GROMACS users
Subject: Re: [gmx-users] Index file

These are the last line of my gro file:

5SOLHW299818   7.429   8.372  11.524
5CL  CL99819   0.485   3.864  11.451
5CL  CL99820   5.689   6.730   9.692
   9.21490   8.92980  12.40750


Here, I brought you the output of make_ndx command. As you see CL ions are not 
recognized here.

 Analysing residue names:
There are:48Protein residues
There are:   238  Other residues
There are: 12624  Water residues
Analysing Protein...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into 
groups...

  0 System  : 99817 atoms
  1 Protein :   720 atoms
  2 Protein-H   :   356 atoms
  3 C-alpha :48 atoms
  4 Backbone:   144 atoms
  5 MainChain   :   190 atoms
  6 MainChain+Cb:   234 atoms
  7 MainChain+H :   240 atoms
  8 SideChain   :   480 atoms
  9 SideChain-H :   166 atoms
 10 Prot-Masses :   720 atoms
 11 non-Protein : 99097 atoms
 12 Other   : 31892 atoms
 13 POPC: 31892 atoms
 14 Water   : 67205 atoms
 15 SOL : 67205 atoms
 16 non-Water   : 32612 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


Somehow confusing for me!


Sincerely,
Shima


----- Original Message -
From: Justin Lemkul 
To: Shima Arasteh ; Discussion list for GROMACS 
users 
Cc:
Sent: Monday, December 31, 2012 8:19 PM
Subject: Re: [gmx-users] Index file



On 12/31/12 11:45 AM, Shima Arasteh wrote:
>
>
> It is 4.5.5.
> I need to say that I had a pdb file which was produced by VMD, May it be the 
> reason of problem?
>
>

Without seeing the aforementioned information (substituting make_ndx screen 
output for editconf command, which is not relevant), it's impossible to say 
anything.  There is no logical reason why ions present in the coordinate file 
(independent of format) do not show up in the selection list and I cannot 
reproduce the problem with any file I have available.  Ions are showing up just 
fine in everything I can see.

-Justin

-- 

Justin A. Lemkul, Ph.D.
Research Scientist
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] Index file

[Justin Lemkul]

On 12/31/12 11:58 AM, Shima Arasteh wrote:

These are the last line of my gro file:

 5SOLHW299818   7.429   8.372  11.524
 5CL  CL99819   0.485   3.864  11.451
 5CL  CL99820   5.689   6.730   9.692
9.21490   8.92980  12.40750


Here, I brought you the output of make_ndx command. As you see CL ions are not 
recognized here.

  Analysing residue names:
There are:48Protein residues
There are:   238  Other residues
There are: 12624  Water residues
Analysing Protein...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into 
groups...

   0 System  : 99817 atoms
   1 Protein :   720 atoms
   2 Protein-H   :   356 atoms
   3 C-alpha :48 atoms
   4 Backbone:   144 atoms
   5 MainChain   :   190 atoms
   6 MainChain+Cb:   234 atoms
   7 MainChain+H :   240 atoms
   8 SideChain   :   480 atoms
   9 SideChain-H :   166 atoms
  10 Prot-Masses :   720 atoms
  11 non-Protein : 99097 atoms
  12 Other   : 31892 atoms
  13 POPC: 31892 atoms
  14 Water   : 67205 atoms
  15 SOL : 67205 atoms
  16 non-Water   : 32612 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


Somehow confusing for me!



It could be that both your last SOL and both CL ions have the same residue
number.  Renumber the file with genconf and try again.  The only other thing I
can think of is that you don't have an entry for CL in residuetypes.dat
indicating that it is an ion.  The "Ion" group should be generated by default
whenever an ion is encountered, but you don't have one.

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] Index file

[Shima Arasteh]

These are the last line of my gro file:

    5SOL    HW299818   7.429   8.372  11.524
    5CL  CL99819   0.485   3.864  11.451
    5CL  CL99820   5.689   6.730   9.692
   9.21490   8.92980  12.40750


Here, I brought you the output of make_ndx command. As you see CL ions are not 
recognized here.

 Analysing residue names:
There are:    48    Protein residues
There are:   238  Other residues
There are: 12624  Water residues
Analysing Protein...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into 
groups...

  0 System  : 99817 atoms
  1 Protein :   720 atoms
  2 Protein-H   :   356 atoms
  3 C-alpha :    48 atoms
  4 Backbone    :   144 atoms
  5 MainChain   :   190 atoms
  6 MainChain+Cb    :   234 atoms
  7 MainChain+H :   240 atoms
  8 SideChain   :   480 atoms
  9 SideChain-H :   166 atoms
 10 Prot-Masses :   720 atoms
 11 non-Protein : 99097 atoms
 12 Other   : 31892 atoms
 13 POPC    : 31892 atoms
 14 Water   : 67205 atoms
 15 SOL : 67205 atoms
 16 non-Water   : 32612 atoms

 nr : group   !   'name' nr name   'splitch' nr    Enter: 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


Somehow confusing for me!


Sincerely,
Shima


----- Original Message -
From: Justin Lemkul 
To: Shima Arasteh ; Discussion list for GROMACS 
users 
Cc: 
Sent: Monday, December 31, 2012 8:19 PM
Subject: Re: [gmx-users] Index file



On 12/31/12 11:45 AM, Shima Arasteh wrote:
> 
> 
> It is 4.5.5.
> I need to say that I had a pdb file which was produced by VMD, May it be the 
> reason of problem?
> 
> 

Without seeing the aforementioned information (substituting make_ndx screen 
output for editconf command, which is not relevant), it's impossible to say 
anything.  There is no logical reason why ions present in the coordinate file 
(independent of format) do not show up in the selection list and I cannot 
reproduce the problem with any file I have available.  Ions are showing up just 
fine in everything I can see.

-Justin

-- 

Justin A. Lemkul, Ph.D.
Research Scientist
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] Index file

[Justin Lemkul]

On 12/31/12 11:45 AM, Shima Arasteh wrote:



It is 4.5.5.
I need to say that I had a pdb file which was produced by VMD, May it be the 
reason of problem?




Without seeing the aforementioned information (substituting make_ndx screen 
output for editconf command, which is not relevant), it's impossible to say 
anything.  There is no logical reason why ions present in the coordinate file 
(independent of format) do not show up in the selection list and I cannot 
reproduce the problem with any file I have available.  Ions are showing up just 
fine in everything I can see.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] Index file

[Shima Arasteh]

It is 4.5.5.
I need to say that I had a pdb file which was produced by VMD, May it be the 
reason of problem?



Sincerely,
Shima



From: Justin Lemkul 
To: Discussion list for GROMACS users  
Sent: Monday, December 31, 2012 7:54 PM
Subject: Re: [gmx-users] Index file



On 12/31/12 11:20 AM, Shima Arasteh wrote:
> No, I see CL ions in gro file after using editconf, but when I want to make 
> an index file, there is not CL option to choose!
> 

What Gromacs version is this?  I cannot reproduce this problem with 4.5.5 or 
the development 4.6 version.  Anything I have with CL in it shows up in the 
make_ndx list.

-Justin

-- 

Justin A. Lemkul, Ph.D.
Research Scientist
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] Index file

[Justin Lemkul]

On 12/31/12 11:20 AM, Shima Arasteh wrote:

No, I see CL ions in gro file after using editconf, but when I want to make an 
index file, there is not CL option to choose!



What Gromacs version is this?  I cannot reproduce this problem with 4.5.5 or the 
development 4.6 version.  Anything I have with CL in it shows up in the make_ndx 
list.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] Index file

[Shima Arasteh]

No, I see CL ions in gro file after using editconf, but when I want to make an 
index file, there is not CL option to choose!




Sincerely,
Shima



From: Justin Lemkul 
To: Shima Arasteh ; Discussion list for GROMACS 
users  
Sent: Monday, December 31, 2012 6:02 PM
Subject: Re: [gmx-users] Index file



On 12/31/12 3:17 AM, Shima Arasteh wrote:
> 
>   I know that I can use pdb and build my index file. But I want to know the 
>problem. What's the problem?
> 

It sounds rather unbelievable that editconf would mysteriously delete atoms. 
There is no way for anyone to say what is going on given the current 
information.  Please post:

1. Your editconf command
2. The first and last few lines of atoms section of the original .pdb file
3. The first and last few lines of the resulting .gro file

-Justin

-- 

Justin A. Lemkul, Ph.D.
Research Scientist
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] Index file

[Justin Lemkul]

On 12/31/12 3:17 AM, Shima Arasteh wrote:


  I know that I can use pdb and build my index file. But I want to know the 
problem. What's the problem?



It sounds rather unbelievable that editconf would mysteriously delete atoms. 
There is no way for anyone to say what is going on given the current 
information.  Please post:


1. Your editconf command
2. The first and last few lines of atoms section of the original .pdb file
3. The first and last few lines of the resulting .gro file

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] Index file

[Shima Arasteh]

 I know that I can use pdb and build my index file. But I want to know the 
problem. What's the problem?

Sincerely,
Shima



From: Chandan Choudhury 
To: Shima Arasteh ; Discussion list for GROMACS 
users  
Sent: Monday, December 31, 2012 11:08 AM
Subject: Re: [gmx-users] Index file







On Mon, Dec 31, 2012 at 1:07 PM, Chandan Choudhury  wrote:


>
>
>
>
>On Mon, Dec 31, 2012 at 11:59 AM, Shima Arasteh  
>wrote:
>
>Dear all,
>>I had a .pdb file containing protein, popc, and ions. So I used editconf to 
>>make a .gro file. But when I want to make an index file, 2 CL ions are not 
>>identified, so I can not choose it.
>>
>>
>use make_ndx f .pdb

use make_ndx -f .pdb


>Sincerely,
>>Shima
>>--
>>gmx-users mailing list    gmx-users@gromacs.org
>>http://lists.gromacs.org/mailman/listinfo/gmx-users
>>* Please search the archive at 
>>http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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>>www interface or send it to gmx-users-requ...@gromacs.org.
>>* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
>--
>Chandan kumar Choudhury
>NCL, Pune
>
>INDIA 
>



--
Chandan kumar Choudhury
NCL, Pune

INDIA   
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Re: [gmx-users] Index file

[Chandan Choudhury]

On Mon, Dec 31, 2012 at 1:07 PM, Chandan Choudhury wrote:

>
>
>
> On Mon, Dec 31, 2012 at 11:59 AM, Shima Arasteh <
> shima_arasteh2...@yahoo.com> wrote:
>
>> Dear all,
>> I had a .pdb file containing protein, popc, and ions. So I used editconf
>> to make a .gro file. But when I want to make an index file, 2 CL ions are
>> not identified, so I can not choose it.
>>
>> use make_ndx f .pdb
>

use make_ndx -f .pdb

>
>
>> Sincerely,
>> Shima
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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>> www interface or send it to gmx-users-requ...@gromacs.org.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
>
> --
> Chandan kumar Choudhury
> NCL, Pune
> INDIA
>
>


--
Chandan kumar Choudhury
NCL, Pune
INDIA
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Re: [gmx-users] Index file

[Chandan Choudhury]

On Mon, Dec 31, 2012 at 11:59 AM, Shima Arasteh  wrote:

> Dear all,
> I had a .pdb file containing protein, popc, and ions. So I used editconf
> to make a .gro file. But when I want to make an index file, 2 CL ions are
> not identified, so I can not choose it.
>
> use make_ndx f .pdb


> Sincerely,
> Shima
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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--
Chandan kumar Choudhury
NCL, Pune
INDIA
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Re: [gmx-users] Index file

[Justin A. Lemkul]

Steven Neumann wrote:

Dear Gmx Users,
 
I want to create index file of my protein residues - each group 
corresponds to different residue. Is there any option in make_ndx which 
will allow me to do it automatically instead of typing: r 180, r 181, 
... r 550?
 


splitres 1

That will split the entire protein group (1, by default) into its residues.

-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] Index file

[Justin A. Lemkul]

swati patel wrote:
Sorry,I did not realized about archive.Yess,It has solutions for many 
errors occuring in gromacs.


But the problem I am facing now is that i made index.idx file.Like in 
your tutorial i merged my protein and ligand group.


And the output is somewhat like this

 [ System ]
   123456789   10   11   12   13   14   15
  16   17   18   19   20

Only a series of numbers are there with no info of groups.

Please tell me how to make correct index file.



Please start by reading the manual.

-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] index file subgroups

[Justin A. Lemkul]

Elisabeth wrote:

Hello,

I am trying to figure out how to plot or obtain the average values of 
Gyration radius from different subgroups of index file. index file 
prompts for a single group and I need to calculate the averages for all 
subgroup by hand.


Is there any way to compute averages or plot all subgroups directly?



Write a loop to call g_gyrate for each group you wish to analyze.

-Justin


g_polystat -f *.trr -s *.tpr -o *.xvg -n *.ndx -w

Thanks,
Regards,



--


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] index file

[Justin A. Lemkul]

ahmet yıldırım wrote:

Dear users,

Firstly thanks for your replies. I have two ligands as I said before.
I will analyze the system together ligands after the simulation is finished.
For example:
I want to plot potential energy of all system (that is, 
protein+LİGA+LİGB) by g_energy.


This is not your whole system.  Per the snippets below, you have water and ions, 
as well.  You cannot decompose the potential in this way.



Then,
Should I create the groups as the following?

*energygrps  = ProteinLİGA_LİGB*
tc-grps = Protein_LİGA_LİGBWater_and_ions



This will break down short-range nonbonded interactions (and nothing else!) 
between protein, LIGA_LIGB, and the rest of the system.



OR

*energygrps  = ProteinLİGALİGB*
tc-grps = Protein_LİGA_LİGBWater_and_ions



This will give you a decomposition between protein, LIGA, LIGB, and the rest of 
the system.  Choose whichever is most appropriate for you.


-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] index file

[ahmet yıldırım]

Dear users,

Firstly thanks for your replies. I have two ligands as I said before.
I will analyze the system together ligands after the simulation is finished.
For example:
I want to plot potential energy of all system (that is, protein+LİGA+LİGB)
by g_energy.
Then,
Should I create the groups as the following?

*energygrps  = ProteinLİGA_LİGB*
tc-grps = Protein_LİGA_LİGBWater_and_ions

OR

*energygrps  = ProteinLİGALİGB*
tc-grps = Protein_LİGA_LİGBWater_and_ions

Thanks

12 Mayıs 2011 18:29 tarihinde lina  yazdı:

> 2011/5/12 Justin A. Lemkul :
> >
> >
> > lina wrote:
> >>
> >> make_ndx -f your.gro/pdb -n your.ndx -o your.ndx
> >>
> >> LiGA & LİGB:
> >
> > This is not correct.  You need to use | rather than &.  Using logical and
> > (&) means the index group will contain atoms that are common to both LIGA
> > and LIGB.  If they are distinct entities, the group will be empty.
>  Logical
> > or (|) says merge the two different groups to create one unified group.
>
> Ooops
>
>
> >
> > -Justin
> >
> >> q
> >>
> >> in grompp add -n your.ndx
> >>
> >>
> >> 2011/5/12 ahmet yıldırım :
> >>>
> >>> Dear users,
> >>>
> >>> I have two ligands. I created a special index group that merges the
> >>> protein,
> >>> LiGA and LİGB.
> >>>
> >>> I have the pr.mdp file as the following:
> >>> ...
> >>> energygrps  = ProteinLİGA_LİGB
> >>> tc-grps = Protein_LİGA_LİGBWater_and_ions
> >>> ...
> >>>
> >>> grompp -f pr.mdp -p topol.top -c em.gro -n index.ndx -o pr.tpr
> >>> Fatal error:
> >>> Group LİGA_LİGB not found in indexfile.
> >>>
> >>> I get the fatal error since I dont have a special index group that
> merges
> >>> LiGA and LİGB. should I create two different index file?
> >>>
> >>> Thanks in advance
> >>> --
> >>> Ahmet YILDIRIM
> >>>
> >>> --
> >>> gmx-users mailing listgmx-users@gromacs.org
> >>> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >>> Please search the archive at
> >>> http://www.gromacs.org/Support/Mailing_Lists/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.
> >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>>
> >>
> >>
> >>
> >
> > --
> > 
> >
> > 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/Support/Mailing_Lists/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.
> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
>
>
>
> --
> Best Regards,
>
> lina
> --
> gmx-users mailing listgmx-users@gromacs.org
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-- 
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Re: [gmx-users] index file

[lina]

2011/5/12 Justin A. Lemkul :
>
>
> lina wrote:
>>
>> make_ndx -f your.gro/pdb -n your.ndx -o your.ndx
>>
>> LiGA & LİGB:
>
> This is not correct.  You need to use | rather than &.  Using logical and
> (&) means the index group will contain atoms that are common to both LIGA
> and LIGB.  If they are distinct entities, the group will be empty.  Logical
> or (|) says merge the two different groups to create one unified group.

Ooops


>
> -Justin
>
>> q
>>
>> in grompp add -n your.ndx
>>
>>
>> 2011/5/12 ahmet yıldırım :
>>>
>>> Dear users,
>>>
>>> I have two ligands. I created a special index group that merges the
>>> protein,
>>> LiGA and LİGB.
>>>
>>> I have the pr.mdp file as the following:
>>> ...
>>> energygrps      = Protein    LİGA_LİGB
>>> tc-grps         = Protein_LİGA_LİGB    Water_and_ions
>>> ...
>>>
>>> grompp -f pr.mdp -p topol.top -c em.gro -n index.ndx -o pr.tpr
>>> Fatal error:
>>> Group LİGA_LİGB not found in indexfile.
>>>
>>> I get the fatal error since I dont have a special index group that merges
>>> LiGA and LİGB. should I create two different index file?
>>>
>>> Thanks in advance
>>> --
>>> Ahmet YILDIRIM
>>>
>>> --
>>> gmx-users mailing list    gmx-users@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>
>>
>>
>
> --
> 
>
> 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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-- 
Best Regards,

lina
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Re: [gmx-users] index file

[Justin A. Lemkul]

lina wrote:

make_ndx -f your.gro/pdb -n your.ndx -o your.ndx

LiGA & LİGB:


This is not correct.  You need to use | rather than &.  Using logical and (&) 
means the index group will contain atoms that are common to both LIGA and LIGB. 
 If they are distinct entities, the group will be empty.  Logical or (|) says 
merge the two different groups to create one unified group.


-Justin


q

in grompp add -n your.ndx


2011/5/12 ahmet yıldırım :

Dear users,

I have two ligands. I created a special index group that merges the protein,
LiGA and LİGB.

I have the pr.mdp file as the following:
...
energygrps  = ProteinLİGA_LİGB
tc-grps = Protein_LİGA_LİGBWater_and_ions
...

grompp -f pr.mdp -p topol.top -c em.gro -n index.ndx -o pr.tpr
Fatal error:
Group LİGA_LİGB not found in indexfile.

I get the fatal error since I dont have a special index group that merges
LiGA and LİGB. should I create two different index file?

Thanks in advance
--
Ahmet YILDIRIM

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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] index file

[lina]

make_ndx -f your.gro/pdb -n your.ndx -o your.ndx

LiGA & LİGB:
q

in grompp add -n your.ndx


2011/5/12 ahmet yıldırım :
> Dear users,
>
> I have two ligands. I created a special index group that merges the protein,
> LiGA and LİGB.
>
> I have the pr.mdp file as the following:
> ...
> energygrps  = Protein    LİGA_LİGB
> tc-grps = Protein_LİGA_LİGB    Water_and_ions
> ...
>
> grompp -f pr.mdp -p topol.top -c em.gro -n index.ndx -o pr.tpr
> Fatal error:
> Group LİGA_LİGB not found in indexfile.
>
> I get the fatal error since I dont have a special index group that merges
> LiGA and LİGB. should I create two different index file?
>
> Thanks in advance
> --
> Ahmet YILDIRIM
>
> --
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>



-- 
Best Regards,

lina
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Re: [gmx-users] index file

[Mark Abraham]

On 12/05/2011 8:23 AM, ahmet yıldırım wrote:

Dear users,

I have two ligands. I created a special index group that merges the 
protein, LiGA and LİGB.


I have the pr.mdp file as the following:
...
energygrps  = ProteinLİGA_LİGB
tc-grps = Protein_LİGA_LİGBWater_and_ions
...

grompp -f pr.mdp -p topol.top -c em.gro -n index.ndx -o pr.tpr
Fatal error:
Group LİGA_LİGB not found in indexfile.

I get the fatal error since I dont have a special index group that 
merges LiGA and LİGB. should I create two different index file?


You need to give grompp an index file that defines all the groups you 
use. Yours didn't define LIGA_LIGB, so you need to do so, or to change 
your energygrps


Mark
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Re: [gmx-users] index file

[Justin A. Lemkul]

Elisabeth wrote:

Dear gromacs users,

I am planning to produce C-C rdf for my system and I have difficulty 
making the index file with a group of all C in the system, [Carbon] . 
.If there are thousands of atoms in the system do I have to go through 
the top file and note down C atom numbers and use those numbers to make 
a group in the index file? What is the easiest way of doing this using 
make_ndx features..




Using "a C*" at the make_ndx prompt should accomplish what you want.  Type 
"help" at the prompt for more advanced examples.


-Justin


Thank you for your hints..




--


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] index file groups

[Mark Abraham]

On 26/02/2011 3:09 AM, Moeed wrote:



Thank you Mark for your detailed explanation. Sorry if I am
slow in understanding some stuff. I appreciate your patience.

1- I have an inquiry about index groups. If I specify all my
solute chains as a whole in one group [all chains] (including
n chains having m atoms each) and calculate interaction
energies between the following:

[all chains] [all chains]

[all chains] [all solvent] (group with all solvent atoms)

[all solvent] [all solvent]

(so  [all chains] is consisting of atoms  1 to m + atom m+1  
to 2m...)


is there a way to get the same results by defining index
groups as individual chains [chain 1] [chain 2] .. [chain n]?
for example

[chain 1] [all solvent]
+[chain 2] all solvent]
+ chain 3 ..

= ? [all chains] [all solvent]


Sure. GROMACS will let you define up to 256 energy groups. You
just need to construct an appropriate index file. You can then add
them together in whatever way suits you, but you'll need to use
some other tool to post-process what g_energy reports.


 I think you answered my question here. If I understand correctly, 
say  [all chains] [all chains] LJ-SR interaction energy is the sum of 
LJ SR with index file of separate chains. That is:

LJ SR of [chain 1] [chain 1]+
[chain 2] [chain 2]+
[chain 3][chain 3]+
.= [all chains] [all chains] LJ SR


Not in general. There may be cross terms. LJ SR-[chain 1] [chain 1] is 
the sum of the short-range LJ interactions of all pairs of atoms within 
the cutoff where both are in chain 1 (ignoring exclusions). LJ SR-[all 
chains] [ all chains] is the sum of the short-range LJ interactions of 
all pairs of atoms within the cutoff where each member of the pair can 
come from *any* chain. For example, if chain 1 is close enough to chain 
2, then their atoms will interact. These will contribute to the RHS of 
your equation, but not the LHS.




In other words [all chains] looks at individual chains ([atoms 1
to m] + [atoms (m+1) to 2m] +...) but what it reports is sum over
all individual chains?



2- The energy units are KJ per mol systems. I think this unit is
not helpful  since in literature what we see is energy of a
quantity per mol in usual sense.


What's the "usual sense" in which an energy of a binary mixture is 
reported?



So my question is how can I get units in mol of particles for a
binary mixture? on the list I read gromacs just divides energies
by avogadros number...Does this mean there is no way of getting
quantities in "mol" for mixtures?


What energy quantities are measured in "mol"?
See http://www.mail-archive.com/gmx-users@gromacs.org/msg27382.html 
for discussion.
Actually I was referring to the same post :) By "usual sense" I mean 
Avogadro number of particles. What I was trying to say is that, In 
literature we see thermodynamic quantities per mol (N_A particles). I 
dont think they report say heat of capacity per mole of systems..(what 
gromcs calculates). 


Thermodynamic tables don't report total energies either. Those are 
*extensive* by definition. GROMACS energies are saying that if you had a 
mole of such systems, that would have an energy whose magnitude is that 
reported by GROMACS. So the actual system has an energy whose magnitude 
is smaller by a factor of N_A.


We always see experimental data in mole amount of substance.for pure 
systems, the values g_energy give should be divided by nmol (no of 
particles) to get values per mole of sunstnce and not system. 
For a binary mixture or ternary system, can we do the same thing by 
dividing by N_A? What I am interested in is interaction energies 
between my polymer and solvent. If I define my all chains as [all 
chains] and get LJ SR and coulomb SR for [all chains] [all chains], in 
order to ba able to compare this with those reported in literature, I 
need to divide by N_A?


I can't say, I've no idea with what you think you can compare this 
computed quantity.



3- If I run a simulation with one chain the interaction energy
is smaller than a system with two chains..in fact there should
be one  specific value for interaction of component A with B
independent of system size and number of particles. This is
again a matter of units I think..How can I calculate the
actual energies for a specific system so that they can be
compared with those in literature (KJ/mol)!


Energies are dependent on system configuration and size. You have
to make sure you are comparing like quantities, e.g. by
normalizing with respect to the number of interacting chains, or
atoms or whatever. I do not understand any sense in which your
assertions above are true.


 Tsorry I was not clear with my question..As I mentioned just above, 
by normalizing you mean dividing by

Re: [gmx-users] index file groups

[Moeed]

>
> Thank you Mark for your detailed explanation. Sorry if I am slow in
>> understanding some stuff. I appreciate your patience.
>>
>> 1- I have an inquiry about index groups. If I specify all my solute chains
>> as a whole in one group [all chains] (including n chains having m atoms
>> each) and calculate interaction energies between the following:
>>
>> [all chains] [all chains]
>>
>> [all chains] [all solvent] (group with all solvent atoms)
>>
>> [all solvent] [all solvent]
>>
>> (so  [all chains] is consisting of atoms  1 to m + atom m+1   to 2m...)
>>
>> is there a way to get the same results by defining index groups as
>> individual chains [chain 1] [chain 2] .. [chain n]? for example
>>
>> [chain 1] [all solvent]
>> +[chain 2] all solvent]
>> + chain 3 ..
>>
>> = ? [all chains] [all solvent]
>>
>
> Sure. GROMACS will let you define up to 256 energy groups. You just need to
> construct an appropriate index file. You can then add them together in
> whatever way suits you, but you'll need to use some other tool to
> post-process what g_energy reports.


 I think you answered my question here. If I understand correctly, say  [all
chains] [all chains] LJ-SR interaction energy is the sum of LJ SR with index
file of separate chains. That is:
LJ SR of [chain 1] [chain 1]+
[chain 2] [chain 2]+

> [chain 3][chain 3]+
>
.= [all chains] [all chains] LJ SR

>
> In other words [all chains] looks at individual chains ([atoms 1 to m] +
> [atoms (m+1) to 2m] +...) but what it reports is sum over all individual
> chains?
>



>  2- The energy units are KJ per mol systems. I think this unit is not
>> helpful  since in literature what we see is energy of a quantity per mol in
>> usual sense.
>>
>
> What's the "usual sense" in which an energy of a binary mixture is
> reported?
>
>
>  So my question is how can I get units in mol of particles for a binary
>> mixture? on the list I read gromacs just divides energies by avogadros
>> number...Does this mean there is no way of getting quantities in "mol" for
>> mixtures?
>>
>
> What energy quantities are measured in "mol"?
>
> See http://www.mail-archive.com/gmx-users@gromacs.org/msg27382.html for
> discussion.
>
> Actually I was referring to the same post :) By "usual sense" I mean
> Avogadro number of particles. What I was trying to say is that, In
> literature we see thermodynamic quantities per mol (N_A particles). I dont
> think they report say heat of capacity per mole of systems..(what gromcs
> calculates). We always see experimental data in mole amount of substance.for
> pure systems, the values g_energy give should be divided by nmol (no of
> particles) to get values per mole of sunstnce and not system.
>

For a binary mixture or ternary system, can we do the same thing by dividing
by N_A? What I am interested in is interaction energies between my polymer
and solvent. If I define my all chains as [all chains] and get LJ SR and
coulomb SR for [all chains] [all chains], in order to ba able to compare
this with those reported in literature, I need to divide by N_A?



>  3- If I run a simulation with one chain the interaction energy is smaller
>> than a system with two chains..in fact there should be one  specific value
>> for interaction of component A with B independent of system size and number
>> of particles. This is again a matter of units I think..How can I calculate
>> the actual energies for a specific system so that they can be compared with
>> those in literature (KJ/mol)!
>>
>
> Energies are dependent on system configuration and size. You have to make
> sure you are comparing like quantities, e.g. by normalizing with respect to
> the number of interacting chains, or atoms or whatever. I do not understand
> any sense in which your assertions above are true.


 Tsorry I was not clear with my question..As I mentioned just above, by
normalizing you mean dividing by -nmol? If yes, for ternary system, I need
to divide by N-A oly?

>
>
>  4- Again regarding index groups, I am trying to realize how gromacs deals
>> with a number of chains  defined as awhole in a group [all chains]. For
>> instance for Rg or end to end distance, what is calculated based on [all
>> chains] is the average of the case with index file having
>> [chain 1] [chain n]?
>>
>
> You can calculate an end-to-end distance of a chain in a configuration. You
> can observe the average of that quantity over a set of configurations. You
> can compute that average over different sets of configurations, and average
> over those if you want to. But in what sense is the "end-to-end distance
> based on [all chains]" meaningful?


 By this question I was again trying to realize how calculations are done by
specifying two different index files ( case 1: [all chains] and case 2:
[chain 1] [chain 2]...)

As in question 1 above : for end to end distance does [all chains] looks at
indivdual subchains and takes the average of Rg or End to end sidtance over
chains or it looks at them as a whole group (a sin

Re: [gmx-users] index file groups

[Mark Abraham]

On 25/02/2011 6:37 PM, Nick wrote:

Hello to all,

Please help me with the following questions. Your attention is greatly 
appreciated.


1- I have an inquiry about index groups. If I specify all my solute 
chains as a whole in one group [all chains] (including n chains having 
m atoms each) and calculate interaction energies between the following:


[all chains] [all chains]

[all chains] [all solvent] (group with all solvent atoms)

[all solvent] [all solvent]

(so  [all chains] is consisting of atoms  1 to m + atom m+1   to 2m...)

is there a way to get the same results by defining index groups as 
individual chains [chain 1] [chain 2] .. [chain n]? for example


[chain 1] [all solvent]
+[chain 2] all solvent]
+ chain 3 ..

= ? [all chains] [all solvent]


Sure. GROMACS will let you define up to 256 energy groups. You just need 
to construct an appropriate index file. You can then add them together 
in whatever way suits you, but you'll need to use some other tool to 
post-process what g_energy reports.


2- The energy units are KJ per mol systems. I think this unit is not 
helpful  since in literature what we see is energy of a quantity per 
mol in usual sense. 


What's the "usual sense" in which an energy of a binary mixture is reported?

So my question is how can I get units in mol of particles for a binary 
mixture? on the list I read gromacs just divides energies by avogadros 
number...Does this mean there is no way of getting quantities in "mol" 
for mixtures?


What energy quantities are measured in "mol"?

See http://www.mail-archive.com/gmx-users@gromacs.org/msg27382.html for 
discussion.


3- If I run a simulation with one chain the interaction energy is 
smaller than a system with two chains..in fact there should be one  
specific value for interaction of component A with B independent of 
system size and number of particles. This is again a matter of units I 
think..How can I calculate the actual energies for a specific system 
so that they can be compared with those in literature (KJ/mol)!


Energies are dependent on system configuration and size. You have to 
make sure you are comparing like quantities, e.g. by normalizing with 
respect to the number of interacting chains, or atoms or whatever. I do 
not understand any sense in which your assertions above are true.


4- Again regarding index groups, I am trying to realize how gromacs 
deals with a number of chains  defined as awhole in a group [all 
chains]. For instance for Rg or end to end distance, what is 
calculated based on [all chains] is the average of the case with index 
file having

[chain 1] [chain n]?


You can calculate an end-to-end distance of a chain in a configuration. 
You can observe the average of that quantity over a set of 
configurations. You can compute that average over different sets of 
configurations, and average over those if you want to. But in what sense 
is the "end-to-end distance based on [all chains]" meaningful?


In other words [all chains] deals with all chains separately and 
reports quantities for ALL the chains as a group?


If you give a GROMACS tool a set of atoms over which to do an operation, 
it does that operation over that set of atoms. If that operation doesn't 
make sense on that set of atoms, then you've asked for a nonsense 
operation, and the problem does not lie with GROMACS. If you want the 
average of the end-to-end distance of all your chains over your 
simulation, then you'll have to compute the time-average for each chain 
individually, and then take the chain-average of them.


Mark
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Re: [gmx-users] index file for interaction energies

[Justin A. Lemkul]

Nick wrote:

One last question!

1- So what are the 12 energy terms I get by passing index file onto step 
2 below?  I ignored rerun! what does rerun does?





I don't know what 12 terms you're referring to.  You'll get A-A, A-B, and B-B 
short-range nonbonded terms, the exact enumeration of which will depend on the 
settings in your .mdp file.


The -rerun function is explained in the manual, or alternatively "mdrun -h."  I 
assumed (perhaps incorrectly) that you had generated a trajectory using some 
energygrps and you wished to make changes after the fact in the way the 
nonbonded potential was decomposed.


2- So I dont have to include index file in mdrun initially..In brief 
what I need is:



step 1  grompp .(no index)

step 2  mdrun -s old.tpr   -o old.trr   -c *.gro

(grompp and mdrun  as usual) then:

 grompp  -f energygroups.mdp -c .top   -o 
new.tpr  * -n index.ndx*


   mdrun   *-s new.tpr  -rerun old.trr...*


Please confirm. Many thanks for your help.



You don't necessarily need the -rerun function if you plan ahead.  Using mdrun 
-rerun is only useful in the case that you haven't set your energygrps properly 
and you don't want to completely run the simulation over again.


-Justin





On 22 February 2011 17:35, Justin A. Lemkul > wrote:




Nick wrote:


Dear Justin,

Thanks for your reply and Sorry for asking naive questions...




1- I am looking at all possible interaction energies between
components A and B. that is A-A AB and BB. So interaction
between single chains is not what I want. With this I think my
initial approach was right. That is putting all atoms of 3 A
chains under [A] and the same all solvent atoms under [B] and
setting A and B as energy groups in mdp. Am I right?


If you don't want your energies on a per-chain basis, then yes.


2- One more thing bout question 3: I am passing on index.ndx to
mdrun command.

with the index file I talked about I am getting the follwoing
for AA AB and BB: LJ SR, LJ 1-4 coulomb SR and 1-4. (i.e 12
energy terms).

I think you say I need rerun since you assumed I did not pass it
onto mdrun. right?


You need to create a new .tpr file that has the desired groups
specified in it.  You pass the new .tpr file to mdrun, in
conjunction with your old trajectory (i.e., mdrun -s new.tpr -rerun
old.trr).


3- to get intermolecular interaction energies say for AA I need
to add up LJ SR+coulomb SR? say +123-50=73 ? or just take
absolute values : 123+50=173 ?


Sign matters a lot.  Positive is repulsive, negative is attractive.
 You can't just switch them arbitrarily.

-Justin

Thanks,



   Nick wrote:

   Dear experts,

   1- I am trying to get interaction energies between solute (3
   chains A) and solvent 50 molecules B. In the index file I
   created two groups: one for all atoms of [A] and and [B]
for all
   solvent molecules. and by setting A and B as energy groups in
   mdp file I am getting break down as A-A, A-B and B-B with
g_energy.

   I am a little confused as I dont know if I need to create
   different groups for my solute to get interaction
energies A-A,
   A-B and B-B. I mean do I need to have [A1] for solute chain 1
   ...[A3] for chain 3?


   If you want a breakdown of per-chain energetics, then yes,
specify
   each chain as a group.  The programs will only do what you tell
   them, nothing more, nothing less.



 
   and then sent A1, A2, A3 in mdp file and run g_energy? if

I need
   to specify different chains, then to get say A-A should I
   average over all possible A1-A2, A1A3, A2-A3, A1-B,
A2,B...? I
   am really confused ..


   Theoretically, the short-range terms should sum, not average.


   2- I know it is naive question but What does A1-A1 mean?
How can
   one chain interact with itself?


   Without knowing what the chain is, no one can answer this.
Generally, any atoms that are within the short-range cutoff and
   further away than nrexcl bonds contribute to short-range
   interactions.  Long-range interactions (i.e., PME terms)
happen too,
   but you can't decompose that term with energygrps.


   3- Do I need to use mdrun - rerun option to get beakdown
or just
   g_energy gives what I need?


   You need to -rerun.  g_energy does not take an index file, and it
   only analyzes existing groups, it cannot derive new ones.

   -Justin


   Th

Re: [gmx-users] index file for interaction energies

[Nick]

One last question!

1- So what are the 12 energy terms I get by passing index file onto step 2
below?  I ignored rerun! what does rerun does?


2- So I dont have to include index file in mdrun initially..In brief what I
need is:


step 1  grompp .(no index)

step 2  mdrun -s old.tpr   -o old.trr   -c *.gro

(grompp and mdrun  as usual) then:

 grompp  -f energygroups.mdp -c .top   -o new.tpr
*-n index.ndx
*
mdrun   *-s new.tpr  -rerun old.trr...*


Please confirm. Many thanks for your help.




On 22 February 2011 17:35, Justin A. Lemkul  wrote:

>
>
> Nick wrote:
>
>>
>> Dear Justin,
>>
>> Thanks for your reply and Sorry for asking naive questions...
>>
>


>> 1- I am looking at all possible interaction energies between components A
>> and B. that is A-A AB and BB. So interaction between single chains is not
>> what I want. With this I think my initial approach was right. That is
>> putting all atoms of 3 A chains under [A] and the same all solvent atoms
>> under [B] and setting A and B as energy groups in mdp. Am I right?
>>
>>
> If you don't want your energies on a per-chain basis, then yes.
>
>
>  2- One more thing bout question 3: I am passing on index.ndx to mdrun
>> command.
>>
>> with the index file I talked about I am getting the follwoing for AA AB
>> and BB: LJ SR, LJ 1-4 coulomb SR and 1-4. (i.e 12 energy terms).
>>
>> I think you say I need rerun since you assumed I did not pass it onto
>> mdrun. right?
>>
>>
> You need to create a new .tpr file that has the desired groups specified in
> it.  You pass the new .tpr file to mdrun, in conjunction with your old
> trajectory (i.e., mdrun -s new.tpr -rerun old.trr).
>
>
>  3- to get intermolecular interaction energies say for AA I need to add up
>> LJ SR+coulomb SR? say +123-50=73 ? or just take absolute values : 123+50=173
>> ?
>>
>>
> Sign matters a lot.  Positive is repulsive, negative is attractive.  You
> can't just switch them arbitrarily.
>
> -Justin
>
>  Thanks,
>>
>>
>>
>>Nick wrote:
>>
>>Dear experts,
>>
>>1- I am trying to get interaction energies between solute (3
>>chains A) and solvent 50 molecules B. In the index file I
>>created two groups: one for all atoms of [A] and and [B] for all
>>solvent molecules. and by setting A and B as energy groups in
>>mdp file I am getting break down as A-A, A-B and B-B with g_energy.
>>
>>I am a little confused as I dont know if I need to create
>>different groups for my solute to get interaction energies A-A,
>>A-B and B-B. I mean do I need to have [A1] for solute chain 1
>>...[A3] for chain 3?
>>
>>
>>If you want a breakdown of per-chain energetics, then yes, specify
>>each chain as a group.  The programs will only do what you tell
>>them, nothing more, nothing less.
>>
>>
>>
>>
>>and then sent A1, A2, A3 in mdp file and run g_energy? if I need
>>to specify different chains, then to get say A-A should I
>>average over all possible A1-A2, A1A3, A2-A3, A1-B, A2,B...? I
>>am really confused ..
>>
>>
>>Theoretically, the short-range terms should sum, not average.
>>
>>
>>2- I know it is naive question but What does A1-A1 mean? How can
>>one chain interact with itself?
>>
>>
>>Without knowing what the chain is, no one can answer this.
>> Generally, any atoms that are within the short-range cutoff and
>>further away than nrexcl bonds contribute to short-range
>>interactions.  Long-range interactions (i.e., PME terms) happen too,
>>but you can't decompose that term with energygrps.
>>
>>
>>3- Do I need to use mdrun - rerun option to get beakdown or just
>>g_energy gives what I need?
>>
>>
>>You need to -rerun.  g_energy does not take an index file, and it
>>only analyzes existing groups, it cannot derive new ones.
>>
>>-Justin
>>
>>
>>Thanks for your help
>>Paniz
>>
>>
>>-- 
>>
>>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/Support/Mailing_Lists/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
>>.
>>
>>Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>>
> --
> 
>
> Justin

Re: [gmx-users] index file for interaction energies

[Justin A. Lemkul]

Nick wrote:


Dear Justin,

Thanks for your reply and Sorry for asking naive questions...

1- I am looking at all possible interaction energies between components 
A and B. that is A-A AB and BB. So interaction between single chains is 
not what I want. With this I think my initial approach was right. That 
is putting all atoms of 3 A chains under [A] and the same all solvent 
atoms under [B] and setting A and B as energy groups in mdp. Am I right?




If you don't want your energies on a per-chain basis, then yes.

2- One more thing bout question 3: I am passing on index.ndx to mdrun 
command.


with the index file I talked about I am getting the follwoing for AA AB 
and BB: LJ SR, LJ 1-4 coulomb SR and 1-4. (i.e 12 energy terms).


I think you say I need rerun since you assumed I did not pass it onto 
mdrun. right?




You need to create a new .tpr file that has the desired groups specified in it. 
 You pass the new .tpr file to mdrun, in conjunction with your old trajectory 
(i.e., mdrun -s new.tpr -rerun old.trr).


3- to get intermolecular interaction energies say for AA I need to add 
up LJ SR+coulomb SR? say +123-50=73 ? or just take absolute values : 
123+50=173 ?




Sign matters a lot.  Positive is repulsive, negative is attractive.  You can't 
just switch them arbitrarily.


-Justin


Thanks,



Nick wrote:

Dear experts,

1- I am trying to get interaction energies between solute (3
chains A) and solvent 50 molecules B. In the index file I
created two groups: one for all atoms of [A] and and [B] for all
solvent molecules. and by setting A and B as energy groups in
mdp file I am getting break down as A-A, A-B and B-B with g_energy.

I am a little confused as I dont know if I need to create
different groups for my solute to get interaction energies A-A,
A-B and B-B. I mean do I need to have [A1] for solute chain 1
...[A3] for chain 3?


If you want a breakdown of per-chain energetics, then yes, specify
each chain as a group.  The programs will only do what you tell
them, nothing more, nothing less.



 


and then sent A1, A2, A3 in mdp file and run g_energy? if I need
to specify different chains, then to get say A-A should I
average over all possible A1-A2, A1A3, A2-A3, A1-B, A2,B...? I
am really confused ..


Theoretically, the short-range terms should sum, not average.


2- I know it is naive question but What does A1-A1 mean? How can
one chain interact with itself?


Without knowing what the chain is, no one can answer this.
 Generally, any atoms that are within the short-range cutoff and
further away than nrexcl bonds contribute to short-range
interactions.  Long-range interactions (i.e., PME terms) happen too,
but you can't decompose that term with energygrps.


3- Do I need to use mdrun - rerun option to get beakdown or just
g_energy gives what I need?


You need to -rerun.  g_energy does not take an index file, and it
only analyzes existing groups, it cannot derive new ones.

-Justin


Thanks for your help
Paniz


-- 



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] index file for interaction energies

[Nick]

Dear Justin,

Thanks for your reply and Sorry for asking naive questions...

1- I am looking at all possible interaction energies between components A
and B. that is A-A AB and BB. So interaction between single chains is not
what I want. With this I think my initial approach was right. That is
putting all atoms of 3 A chains under [A] and the same all solvent atoms
under [B] and setting A and B as energy groups in mdp. Am I right?

2- One more thing bout question 3: I am passing on index.ndx to mdrun
command.

with the index file I talked about I am getting the follwoing for AA AB and
BB: LJ SR, LJ 1-4 coulomb SR and 1-4. (i.e 12 energy terms).

I think you say I need rerun since you assumed I did not pass it onto mdrun.
right?

3- to get intermolecular interaction energies say for AA I need to add up LJ
SR+coulomb SR? say +123-50=73 ? or just take absolute values : 123+50=173 ?

Thanks,


>
> Nick wrote:
>
>> Dear experts,
>>
>> 1- I am trying to get interaction energies between solute (3 chains A) and
>> solvent 50 molecules B. In the index file I created two groups: one for all
>> atoms of [A] and and [B] for all solvent molecules. and by setting A and B
>> as energy groups in mdp file I am getting break down as A-A, A-B and B-B
>> with g_energy.
>>
>> I am a little confused as I dont know if I need to create different groups
>> for my solute to get interaction energies A-A, A-B and B-B. I mean do I need
>> to have [A1] for solute chain 1 ...[A3] for chain 3?
>>
>>
> If you want a breakdown of per-chain energetics, then yes, specify each
> chain as a group.  The programs will only do what you tell them, nothing
> more, nothing less.
>
>
>


>  and then sent A1, A2, A3 in mdp file and run g_energy? if I need to
>> specify different chains, then to get say A-A should I average over all
>> possible A1-A2, A1A3, A2-A3, A1-B, A2,B...? I am really confused ..
>>
>>
> Theoretically, the short-range terms should sum, not average.
>
>
>  2- I know it is naive question but What does A1-A1 mean? How can one chain
>> interact with itself?
>>
>>
> Without knowing what the chain is, no one can answer this.  Generally, any
> atoms that are within the short-range cutoff and further away than nrexcl
> bonds contribute to short-range interactions.  Long-range interactions
> (i.e., PME terms) happen too, but you can't decompose that term with
> energygrps.
>
>
>  3- Do I need to use mdrun - rerun option to get beakdown or just g_energy
>> gives what I need?
>>
>>
> You need to -rerun.  g_energy does not take an index file, and it only
> analyzes existing groups, it cannot derive new ones.
>
> -Justin
>
>
>  Thanks for your help
>> Paniz
>>
>>
> --
> 
>
> 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/Support/Mailing_Lists/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.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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Re: [gmx-users] index file for interaction energies

[Justin A. Lemkul]

Nick wrote:

Dear experts,

1- I am trying to get interaction energies between solute (3 chains A) 
and solvent 50 molecules B. In the index file I created two groups: one 
for all atoms of [A] and and [B] for all solvent molecules. and by 
setting A and B as energy groups in mdp file I am getting break down as 
A-A, A-B and B-B with g_energy.


I am a little confused as I dont know if I need to create different 
groups for my solute to get interaction energies A-A, A-B and B-B. I 
mean do I need to have [A1] for solute chain 1 ...[A3] for chain 3?




If you want a breakdown of per-chain energetics, then yes, specify each chain as 
a group.  The programs will only do what you tell them, nothing more, nothing less.


and then sent A1, A2, A3 in mdp file and run g_energy? if I need to 
specify different chains, then to get say A-A should I average over all 
possible A1-A2, A1A3, A2-A3, A1-B, A2,B...? I am really confused ..




Theoretically, the short-range terms should sum, not average.

2- I know it is naive question but What does A1-A1 mean? How can one 
chain interact with itself?




Without knowing what the chain is, no one can answer this.  Generally, any atoms 
that are within the short-range cutoff and further away than nrexcl bonds 
contribute to short-range interactions.  Long-range interactions (i.e., PME 
terms) happen too, but you can't decompose that term with energygrps.


3- Do I need to use mdrun - rerun option to get beakdown or just 
g_energy gives what I need?




You need to -rerun.  g_energy does not take an index file, and it only analyzes 
existing groups, it cannot derive new ones.


-Justin


Thanks for your help
Paniz



--


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] index file and freezegrps

[Justin A. Lemkul]

Jamie Seyed wrote:

http://oldwiki.gromacs.org/index.php/g_order and I deleted extra groups. 


As a general point, the manual pages for specific tools are often only 
applicable to those specific tools :)


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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] index file and freezegrps

[David van der Spoel]

Jamie Seyed wrote:

Dear all,
I have a question about groups in index-file. For making an index file 
for freezing some atoms, I used procedure like 
http://oldwiki.gromacs.org/index.php/g_order and I deleted extra groups. 
I added freezegrp and freezedim in my em.mdp and I did em step. Then I 
jumped to md step (because there is no need for pr step since I freezing 
atoms), so I added the same lines in md.mdp and I got an error in grompp 
run. Obviously in md.mdp since I have tc_grps I will get this error, 
since I need all the groups that are defined in tc_grps in index file, 
and this will be always required, right? So what is the meaning of "all 
programs can generate default index groups" from man-page?? It seems to 
me the index file should contains all groups to prevent any error, not 
just desired groups... Please correct me if something is missing or 
wrong in my procedure or my conclusion. Many Thanks in Advance/Jamie


If you specify an index file no automatic generation is done. So you 
need to specify all groups that you use in the index file (e.g. Protein, 
System etc.).





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--
David.

David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
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RE: [gmx-users] index file for DPPC

[Kukol, Andreas]

Dear Caty,

You have to make an index file containing groups for each type of atom in one 
of your tails (e.g. the sn1-chain), that means for dppc you end up with 15 
groups: C11, C12, C13, ...
Each group will have 100 elements.

For the sn2-chain you need to make a separate index file.

Andreas

>>>
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On 
Behalf Of koukouli...@eie.gr
Sent: 22 January 2009 11:15
To: gmx-users@gromacs.org
Subject: [gmx-users] index file for DPPC

Dear all gmx_users,

I want to calculate the order parameter after the incorporation of a molecule 
of DHA in the DPPC Bilayer (100 DPPC lipids).

I have read in the manual that the program can gives an idea of the ordering of 
a molecule from head to tail and I have read that I have to construct an index 
file, but I don't know how I can group all the CH2 segments that are necessery 
for this calculation.

I will appreciate your help,

thanks in advance!

Caty.



Dr. Koukoulitsa Catherine
Laboratory of Molecular Analysis
Institute of Organic & Phamaceutical Chemistry
Hellenic National Research Foundation
Vas. Konstantinou 48
11635, Athens
Greece

Tel: +30-210-7273869-71
Fax: +30-210-7273872
Web: www.eie.gr
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Re: [gmx-users] index file for DPPC

[Justin A. Lemkul]

koukouli...@eie.gr wrote:

Dear all gmx_users,
 
I want to calculate the order parameter after the incorporation of a 
molecule of DHA in the DPPC Bilayer (100 DPPC lipids).
 
I have read in the manual that the program can gives an idea of the 
ordering of a molecule from head to tail and I have read that I have to 
construct an index file, but I don't know how I can group all the CH2 
segments that are necessery for this calculation.
 


There is an exact how-to on the wiki site:

http://wiki.gromacs.org/index.php/make_ndx

-Justin


I will appreciate your help,
 
thanks in advance!
 
Caty. 
 
 
 
Dr. Koukoulitsa Catherine

Laboratory of Molecular Analysis
Institute of Organic & Phamaceutical Chemistry
Hellenic National Research Foundation
Vas. Konstantinou 48
11635, Athens
Greece
 
Tel: +30-210-7273869-71

Fax: +30-210-7273872
Web: www.eie.gr 




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--


Justin A. Lemkul
Graduate Research Assistant
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] index file for g_order

[Arneh Babakhani]

Ok great, will do, thanks for your help!

Alan Dodd wrote:

Well, for the terminal methyl, you have no way of
knowing which way the hydrogeons are pointing... So
no.  However, it is worth including the carbonyl
carbon (although it has no hydrogeons, so no order
parameter), as a reference point for the next carbon
down.

--- Arneh Babakhani <[EMAIL PROTECTED]>
wrote:

  

Hi Alan, great, thanks, I suspected something like
that.

Then, is there a way to calculate the Scd order
parameters for these 
carbons, given that there are no explicit

hydrogens???

Arneh

Alan Dodd wrote:

The first and last carbons are not calculated. 
GROMACS needs to use a C-C bond on either side of
  

each


carbon to place the hydrogens, and hence calculate
  

the


order parameter.

--- Arneh Babakhani <[EMAIL PROTECTED]>
wrote:

  
  

Hello,

Now with the g_order bug fixed (see bugzilla #84)


,

I'm trying to 
calculate the orderparameters for 13 carbon atoms


of

the the sn2 chain 
(carbons 2B thru 2N) of a DMPC membrane.   So I
create an index file, 
make a group for each type of carbon, then run

g_order.

The groups in the index file are recognized (as


can

be seen below, where 
I've pasted an excerpt from my terminal).  All 13
carbon groups are there. 


But the output is a list of order parameters for
only 11 carbons (I 
think the last two groups, C2M and C2N, are
truncated off).   Is this 
right? If so, how do I calculate the order
parameters for C2M and C2N ?  
Or, is this another bug?


Thanks,

Arneh

---
Taking z axis as normal to the membrane
Reading file ../FullMD1.tpr, VERSION 3.1.4


(single


precision)
Note: tpx file_version 24, software version 40
Note: nLincsIter not in run input file, setting


it


to 1
Using following groups:
Groupname: C2B First atomname: C2B First atomnr


16


Groupname: C2C First atomname: C2C First atomnr


17


Groupname: C2D First atomname: C2D First atomnr


18


Groupname: C2E First atomname: C2E First atomnr


19


Groupname: C2F First atomname: C2F First atomnr


20


Groupname: C2G First atomname: C2G First atomnr


21


Groupname: C2H First atomname: C2H First atomnr


22


Groupname: C2I First atomname: C2I First atomnr


23


Groupname: C2J First atomname: C2J First atomnr


24


Groupname: C2K First atomname: C2K First atomnr


25


Groupname: C2L First atomname: C2L First atomnr


26


Groupname: C2M First atomname: C2M First atomnr


27


Groupname: C2N First atomname: C2N First atomnr


28


trn version: GMX_trn_file (single precision)
Reading frame   0 time0.000   Number of
elements in first group: 128
Last frame150 time  150.000

Read trajectory. Printing parameters to file
Atom 1 Tensor: x=-0.225996 , y=-0.226754,


z=0.452751


Atom 2 Tensor: x=-0.22165 , y=-0.246523,


z=0.468173


Atom 3 Tensor: x=-0.229328 , y=-0.215539,


z=0.444867


Atom 4 Tensor: x=-0.230127 , y=-0.199614,


z=0.429741


Atom 5 Tensor: x=-0.24599 , y=-0.185492,


z=0.431482


Atom 6 Tensor: x=-0.221037 , y=-0.179952,


z=0.400989


Atom 7 Tensor: x=-0.226934 , y=-0.170633,


z=0.397566


Atom 8 Tensor: x=-0.203112 , y=-0.165726,


z=0.368838


Atom 9 Tensor: x=-0.191929 , y=-0.145227,


z=0.337156


Atom 10 Tensor: x=-0.164109 , y=-0.118401,


z=0.28251


Atom 11 Tensor: x=-0.154092 , y=-0.0753129,
z=0.229405

Back Off! I just backed up order.xvg to
./#order.xvg.11#

Back Off! I just backed up deuter.xvg to
./#deuter.xvg.7#

gcq#146: "We All Get the Flu, We All Get Aids"
(LIVE)

[EMAIL PROTECTED] OrderParameters]$

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Re: [gmx-users] index file for g_order

[Alan Dodd]

Well, for the terminal methyl, you have no way of
knowing which way the hydrogeons are pointing... So
no.  However, it is worth including the carbonyl
carbon (although it has no hydrogeons, so no order
parameter), as a reference point for the next carbon
down.

--- Arneh Babakhani <[EMAIL PROTECTED]>
wrote:

> Hi Alan, great, thanks, I suspected something like
> that.
> 
> Then, is there a way to calculate the Scd order
> parameters for these 
> carbons, given that there are no explicit
> hydrogens???
> 
> Arneh
> 
> Alan Dodd wrote:
> > The first and last carbons are not calculated. 
> > GROMACS needs to use a C-C bond on either side of
> each
> > carbon to place the hydrogens, and hence calculate
> the
> > order parameter.
> >
> > --- Arneh Babakhani <[EMAIL PROTECTED]>
> > wrote:
> >
> >   
> >> Hello,
> >>
> >> Now with the g_order bug fixed (see bugzilla #84)
> ,
> >> I'm trying to 
> >> calculate the orderparameters for 13 carbon atoms
> of
> >> the the sn2 chain 
> >> (carbons 2B thru 2N) of a DMPC membrane.   So I
> >> create an index file, 
> >> make a group for each type of carbon, then run
> >> g_order.
> >>
> >> The groups in the index file are recognized (as
> can
> >> be seen below, where 
> >> I've pasted an excerpt from my terminal).  All 13
> >> carbon groups are there. 
> >>
> >> But the output is a list of order parameters for
> >> only 11 carbons (I 
> >> think the last two groups, C2M and C2N, are
> >> truncated off).   Is this 
> >> right? If so, how do I calculate the order
> >> parameters for C2M and C2N ?  
> >> Or, is this another bug?
> >>
> >> Thanks,
> >>
> >> Arneh
> >>
> >> ---
> >> Taking z axis as normal to the membrane
> >> Reading file ../FullMD1.tpr, VERSION 3.1.4
> (single
> >> precision)
> >> Note: tpx file_version 24, software version 40
> >> Note: nLincsIter not in run input file, setting
> it
> >> to 1
> >> Using following groups:
> >> Groupname: C2B First atomname: C2B First atomnr
> 16
> >> Groupname: C2C First atomname: C2C First atomnr
> 17
> >> Groupname: C2D First atomname: C2D First atomnr
> 18
> >> Groupname: C2E First atomname: C2E First atomnr
> 19
> >> Groupname: C2F First atomname: C2F First atomnr
> 20
> >> Groupname: C2G First atomname: C2G First atomnr
> 21
> >> Groupname: C2H First atomname: C2H First atomnr
> 22
> >> Groupname: C2I First atomname: C2I First atomnr
> 23
> >> Groupname: C2J First atomname: C2J First atomnr
> 24
> >> Groupname: C2K First atomname: C2K First atomnr
> 25
> >> Groupname: C2L First atomname: C2L First atomnr
> 26
> >> Groupname: C2M First atomname: C2M First atomnr
> 27
> >> Groupname: C2N First atomname: C2N First atomnr
> 28
> >>
> >> trn version: GMX_trn_file (single precision)
> >> Reading frame   0 time0.000   Number of
> >> elements in first group: 128
> >> Last frame150 time  150.000
> >>
> >> Read trajectory. Printing parameters to file
> >> Atom 1 Tensor: x=-0.225996 , y=-0.226754,
> z=0.452751
> >> Atom 2 Tensor: x=-0.22165 , y=-0.246523,
> z=0.468173
> >> Atom 3 Tensor: x=-0.229328 , y=-0.215539,
> z=0.444867
> >> Atom 4 Tensor: x=-0.230127 , y=-0.199614,
> z=0.429741
> >> Atom 5 Tensor: x=-0.24599 , y=-0.185492,
> z=0.431482
> >> Atom 6 Tensor: x=-0.221037 , y=-0.179952,
> z=0.400989
> >> Atom 7 Tensor: x=-0.226934 , y=-0.170633,
> z=0.397566
> >> Atom 8 Tensor: x=-0.203112 , y=-0.165726,
> z=0.368838
> >> Atom 9 Tensor: x=-0.191929 , y=-0.145227,
> z=0.337156
> >> Atom 10 Tensor: x=-0.164109 , y=-0.118401,
> z=0.28251
> >> Atom 11 Tensor: x=-0.154092 , y=-0.0753129,
> >> z=0.229405
> >>
> >> Back Off! I just backed up order.xvg to
> >> ./#order.xvg.11#
> >>
> >> Back Off! I just backed up deuter.xvg to
> >> ./#deuter.xvg.7#
> >>
> >> gcq#146: "We All Get the Flu, We All Get Aids"
> >> (LIVE)
> >>
> >> [EMAIL PROTECTED] OrderParameters]$
> >>
> >> ___
> >> gmx-users mailing listgmx-users@gromacs.org
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> >> Please don't post (un)subscribe requests to the
> >> list. Use the 
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> >>
> >> 
> >
> >
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Re: [gmx-users] index file for g_order

[Arneh Babakhani]

Hi Alan, great, thanks, I suspected something like that.

Then, is there a way to calculate the Scd order parameters for these 
carbons, given that there are no explicit hydrogens???


Arneh

Alan Dodd wrote:
The first and last carbons are not calculated. 
GROMACS needs to use a C-C bond on either side of each

carbon to place the hydrogens, and hence calculate the
order parameter.

--- Arneh Babakhani <[EMAIL PROTECTED]>
wrote:

  

Hello,

Now with the g_order bug fixed (see bugzilla #84) ,
I'm trying to 
calculate the orderparameters for 13 carbon atoms of
the the sn2 chain 
(carbons 2B thru 2N) of a DMPC membrane.   So I
create an index file, 
make a group for each type of carbon, then run

g_order.

The groups in the index file are recognized (as can
be seen below, where 
I've pasted an excerpt from my terminal).  All 13
carbon groups are there. 


But the output is a list of order parameters for
only 11 carbons (I 
think the last two groups, C2M and C2N, are
truncated off).   Is this 
right? If so, how do I calculate the order
parameters for C2M and C2N ?  
Or, is this another bug?


Thanks,

Arneh

---
Taking z axis as normal to the membrane
Reading file ../FullMD1.tpr, VERSION 3.1.4 (single
precision)
Note: tpx file_version 24, software version 40
Note: nLincsIter not in run input file, setting it
to 1
Using following groups:
Groupname: C2B First atomname: C2B First atomnr 16
Groupname: C2C First atomname: C2C First atomnr 17
Groupname: C2D First atomname: C2D First atomnr 18
Groupname: C2E First atomname: C2E First atomnr 19
Groupname: C2F First atomname: C2F First atomnr 20
Groupname: C2G First atomname: C2G First atomnr 21
Groupname: C2H First atomname: C2H First atomnr 22
Groupname: C2I First atomname: C2I First atomnr 23
Groupname: C2J First atomname: C2J First atomnr 24
Groupname: C2K First atomname: C2K First atomnr 25
Groupname: C2L First atomname: C2L First atomnr 26
Groupname: C2M First atomname: C2M First atomnr 27
Groupname: C2N First atomname: C2N First atomnr 28

trn version: GMX_trn_file (single precision)
Reading frame   0 time0.000   Number of
elements in first group: 128
Last frame150 time  150.000

Read trajectory. Printing parameters to file
Atom 1 Tensor: x=-0.225996 , y=-0.226754, z=0.452751
Atom 2 Tensor: x=-0.22165 , y=-0.246523, z=0.468173
Atom 3 Tensor: x=-0.229328 , y=-0.215539, z=0.444867
Atom 4 Tensor: x=-0.230127 , y=-0.199614, z=0.429741
Atom 5 Tensor: x=-0.24599 , y=-0.185492, z=0.431482
Atom 6 Tensor: x=-0.221037 , y=-0.179952, z=0.400989
Atom 7 Tensor: x=-0.226934 , y=-0.170633, z=0.397566
Atom 8 Tensor: x=-0.203112 , y=-0.165726, z=0.368838
Atom 9 Tensor: x=-0.191929 , y=-0.145227, z=0.337156
Atom 10 Tensor: x=-0.164109 , y=-0.118401, z=0.28251
Atom 11 Tensor: x=-0.154092 , y=-0.0753129,
z=0.229405

Back Off! I just backed up order.xvg to
./#order.xvg.11#

Back Off! I just backed up deuter.xvg to
./#deuter.xvg.7#

gcq#146: "We All Get the Flu, We All Get Aids"
(LIVE)

[EMAIL PROTECTED] OrderParameters]$

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Re: [gmx-users] index file for g_order

[Alan Dodd]

The first and last carbons are not calculated. 
GROMACS needs to use a C-C bond on either side of each
carbon to place the hydrogens, and hence calculate the
order parameter.

--- Arneh Babakhani <[EMAIL PROTECTED]>
wrote:

> Hello,
> 
> Now with the g_order bug fixed (see bugzilla #84) ,
> I'm trying to 
> calculate the orderparameters for 13 carbon atoms of
> the the sn2 chain 
> (carbons 2B thru 2N) of a DMPC membrane.   So I
> create an index file, 
> make a group for each type of carbon, then run
> g_order.
> 
> The groups in the index file are recognized (as can
> be seen below, where 
> I've pasted an excerpt from my terminal).  All 13
> carbon groups are there. 
> 
> But the output is a list of order parameters for
> only 11 carbons (I 
> think the last two groups, C2M and C2N, are
> truncated off).   Is this 
> right? If so, how do I calculate the order
> parameters for C2M and C2N ?  
> Or, is this another bug?
> 
> Thanks,
> 
> Arneh
> 
> ---
> Taking z axis as normal to the membrane
> Reading file ../FullMD1.tpr, VERSION 3.1.4 (single
> precision)
> Note: tpx file_version 24, software version 40
> Note: nLincsIter not in run input file, setting it
> to 1
> Using following groups:
> Groupname: C2B First atomname: C2B First atomnr 16
> Groupname: C2C First atomname: C2C First atomnr 17
> Groupname: C2D First atomname: C2D First atomnr 18
> Groupname: C2E First atomname: C2E First atomnr 19
> Groupname: C2F First atomname: C2F First atomnr 20
> Groupname: C2G First atomname: C2G First atomnr 21
> Groupname: C2H First atomname: C2H First atomnr 22
> Groupname: C2I First atomname: C2I First atomnr 23
> Groupname: C2J First atomname: C2J First atomnr 24
> Groupname: C2K First atomname: C2K First atomnr 25
> Groupname: C2L First atomname: C2L First atomnr 26
> Groupname: C2M First atomname: C2M First atomnr 27
> Groupname: C2N First atomname: C2N First atomnr 28
> 
> trn version: GMX_trn_file (single precision)
> Reading frame   0 time0.000   Number of
> elements in first group: 128
> Last frame150 time  150.000
> 
> Read trajectory. Printing parameters to file
> Atom 1 Tensor: x=-0.225996 , y=-0.226754, z=0.452751
> Atom 2 Tensor: x=-0.22165 , y=-0.246523, z=0.468173
> Atom 3 Tensor: x=-0.229328 , y=-0.215539, z=0.444867
> Atom 4 Tensor: x=-0.230127 , y=-0.199614, z=0.429741
> Atom 5 Tensor: x=-0.24599 , y=-0.185492, z=0.431482
> Atom 6 Tensor: x=-0.221037 , y=-0.179952, z=0.400989
> Atom 7 Tensor: x=-0.226934 , y=-0.170633, z=0.397566
> Atom 8 Tensor: x=-0.203112 , y=-0.165726, z=0.368838
> Atom 9 Tensor: x=-0.191929 , y=-0.145227, z=0.337156
> Atom 10 Tensor: x=-0.164109 , y=-0.118401, z=0.28251
> Atom 11 Tensor: x=-0.154092 , y=-0.0753129,
> z=0.229405
> 
> Back Off! I just backed up order.xvg to
> ./#order.xvg.11#
> 
> Back Off! I just backed up deuter.xvg to
> ./#deuter.xvg.7#
> 
> gcq#146: "We All Get the Flu, We All Get Aids"
> (LIVE)
> 
> [EMAIL PROTECTED] OrderParameters]$
> 
> ___
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