- 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
&
steh2...@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
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_n
r '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
----- Origin
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 i
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
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
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.
Th
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 curr
t: 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 .g
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 in
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
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.
Sincerely,
Shima
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mai
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
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 ]
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 ]
12345
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 o
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 dire
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 n
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 th
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
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.
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
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
...
g
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.n
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 an
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 m
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
>
> 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 c
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 c
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
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 wh
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
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
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
putt
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 getti
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-
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
I
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
ju
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
>>>>>>>
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
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
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 a
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
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
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
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 try
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 inde
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