On 6/15/13 1:07 PM, Mahin Saberi wrote:
Hi gmx users
I really confused that How I determine the distances between center of mass
of a molecules and center of mass of number of other molecules?
Use g_dist with suitable index groups.
-Justin
--
Justin
On 9/3/12 2:04 AM, Raj wrote:
hi all,
I would like to measure the hydrophobic interaction of the ligand against
the protein during the simulation . From the forum I learnt g_mindist will
be the better tool. But when i used the command g_mindist -f traj.xtc -s
topol.tpr -n index.ndx -on numco
Hi Peter,
Thanks for the reply. I'm not using the contact information at all
(-on is unspecified), and yes, it still generates a result for >6A in
the distance output (-od) , but the result for which atoms are at the
reported distance is sometimes missing from the atom pair output (-o)
file.
MZ
I have not read the source, but the default search radius for mindist is
6A. If you have no contacts within 6A of the atoms in the primary group
to the target group for a given frame, will it still generate a result,
since for all intents and purposes the array search should be null in
that case?
On 9/11/2011 9:09 PM, Steven Neumann wrote:
Dear gmx Users,
I am wondering what is the value of Number of Contacts (<0.6 nm)
between two groups. When I specify one group - Ligand and second
- protein residue - does it count every dostance within 0.6 nm between
every atom from one group and eve
Hi Tsjerk,
i used the command in format-
g_mindist -f md.xtc -s md.tpr -n 13.ndx -od 13.xvg -on 13.xvg -o 13.out -b
500 -e 1500 -d 0.5
so here i obtain the output-
atmpair.out-
0.00e+0013 21161
1.00e+0013 21161
2.00e+0013
On 22/09/2011 4:43 PM, Tsjerk Wassenaar wrote:
Hi Aiswarya,
What did you do, what did you get, what did you expect and what is
your hunch regarding the difference between your result and your
expectation?
And have you checked out g_mindist -h?
Mark
Tsjerk
On Thu, Sep 22, 2011 at 8:21 AM,
Hi Aiswarya,
What did you do, what did you get, what did you expect and what is
your hunch regarding the difference between your result and your
expectation?
Tsjerk
On Thu, Sep 22, 2011 at 8:21 AM, aiswarya pawar
wrote:
> Hi users,
>
> The g_mindist gives the minimum distance between the atoms
ahmet yıldırım wrote:
Dear Justin,
can you suggest me published paper related to about hydrophobic and
hydrophilic contacts?
A few minutes on Google or the literature searching database of your choice
should turn up something useful. If you need to understand the definition or
nature o
Dear Justin,
can you suggest me published paper related to about hydrophobic and
hydrophilic contacts?
03 Temmuz 2011 00:24 tarihinde Justin A. Lemkul yazdı:
>
>
> ahmet yıldırım wrote:
>
>> Dear Justin,
>>
>> You said before "you can obtain some idea by using g_mindist to calculate
>> hydropho
ahmet yıldırım wrote:
Dear Justin,
You said before "you can obtain some idea by using g_mindist to
calculate hydrophobic and hydrophilic contacts between the protein and
ligand".
That is, I can explore whether there is hydrophobic or hydrophilic
feature of ligand using g_mindist tool. is
Chandan Choudhury wrote:
Hi all !!
Can some one clarify me what the g_mindist does. As far as I understood,
it takes two inputs from the index file. If I have more than one entry
in both of the indexes than how would g_mindist function?
g_mindist finds the minimum distance between any two
Ramachandran G wrote:
Hi Gromacs users,
I used g_mindist to calculate the minimum distance between a residue
and a group of water molecules.
Since distance is a length between two points in space, for the program
considers the bunch of water molecules(15 number)
what specific point does
On 9/03/2010 12:22 PM, Justin A. Lemkul wrote:
Dian Jiao wrote:
Hi gmx users,
I was running g_mindist as a batch job for a big number of files on a
pbs cluster. The huge amount of output was redirected to the error
file which has a size limit. Is there way to discard the output of
g_mindist.
Thank you, Justin.
On Mon, Mar 8, 2010 at 6:22 PM, Justin A. Lemkul wrote:
>
>
> Dian Jiao wrote:
>
>> Hi gmx users,
>>
>> I was running g_mindist as a batch job for a big number of files on a pbs
>> cluster. The huge amount of output was redirected to the error file which
>> has a size limit. I
Dian Jiao wrote:
Hi gmx users,
I was running g_mindist as a batch job for a big number of files on a
pbs cluster. The huge amount of output was redirected to the error file
which has a size limit. Is there way to discard the output of g_mindist.
I tried /dev/null as below, it didn't work.
Sorry for the confusion, Tsjerk. Thanks.
On Thu, Mar 4, 2010 at 11:47 AM, Tsjerk Wassenaar wrote:
> Hi Dian,
>
> Now why didn't I guess that you were trying on data obtained from
> Amber?! Maybe because you didn't explicitly mentioned it. It always
> helps to give a full account of what you were
Hi Dian,
Now why didn't I guess that you were trying on data obtained from
Amber?! Maybe because you didn't explicitly mentioned it. It always
helps to give a full account of what you were trying.
Anyway, I don't know the format of the top of my head, so you'll have
to look in another pdb file an
Hi Tsjerk,
My gromacs is 4.0.4.
As it turns out, I do not have a CRYST1 keyword in my pdb file, so I guess
the box is not defined yet. The pdb was taken from the trajectory of AMBER
simulation, so it starts with the keyword "REMARK". How do I include box
dimensions in pdb file then? Just add "CRY
On 4/03/2010 6:38 PM, Tsjerk Wassenaar wrote:
Hi Dian,
Which version of gromacs are you using? Can you assert that the pdb
file has the correct box? It should have a line starting with CRYST1
(grep "^CRYST1" file.pdb). Some versions of gromacs (3.3.2 I think)
didn't write the CRYST1 record, and
Hi Dian,
Which version of gromacs are you using? Can you assert that the pdb
file has the correct box? It should have a line starting with CRYST1
(grep "^CRYST1" file.pdb). Some versions of gromacs (3.3.2 I think)
didn't write the CRYST1 record, and thus disallow PBC related
operations.
Cheers,
The box is 24X24X24 (Angstrom). The dummy atom I added at the end is about
31 A away from the closest water in the box. But if it is periodic,
shouldn't there be waters near the dummy too?
On Wed, Mar 3, 2010 at 10:29 PM, Mark Abraham wrote:
> On 4/03/2010 11:30 AM, Dian Jiao wrote:
>
>> Hi Groma
On 4/03/2010 11:30 AM, Dian Jiao wrote:
Hi Gromacs users,
I was trying to compute minimum distance between groups in a cubic water
box with g_mindist using periodic boundary condition. In order to test
this, I added one more "atom" which is far away from any of the other
atoms in the pdb file. T
Thank you very much Ran,
Will do.
-Shay
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Ran Friedman
Sent: Tuesday, December 22, 2009 16:53
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] g_mindist -or
Dear Shay,
What do you get when -or is present? Do the atoms always belong to the
same residues?
I suspect that since the calculation of the minimal distance is made for
all residues, what you get at the end is the atoms at minimal distance
between the last two residues. This seems like a bug and
Hi Elad,
You can't count on operations that involve PBC after fitting. In your
case, you can use
trjconv -fit translation
to remove translational degrees of freedom only, keeping the system
consistent with PBC.
Hope it helps,
Tsjerk
On Sun, Dec 6, 2009 at 8:50 PM, wrote:
> Hi Tsjerk,
> than
Hi Elad,
This has been mentioned several times before, in a different context.
But fitting only affects coordinates, and not the PBC. So after
fitting the coordinates and the PBC don't match any more and any
analysis requiring PBC, such as calculating minimal distances, will
give garbled results.
Hi Peter,
> Instead of the pairs with the shortest distance a much further pair is
> selected. Although the output pair from "atm-pair.out" has a distance of more
> then 100 Angstrom the value in the file "mindist.xvg" is smaller then one
> Angstrom.
Periodic Boundary Conditions?
You mention
users
Subject: Re: [gmx-users] g_mindist , trajectory only CA atoms, to small
values?
t.peter.muel...@gmx.net wrote:
> Dear Shay, dear Gromacians
>
>> For purposes of debugging this bug you can also use the flag of g_mindist
>> that gives out atom pairs and see which atom pairs is it
t.peter.muel...@gmx.net wrote:
Dear Shay, dear Justin, dear Gromacians
My problem is solved. I used following command
$ g_mindist -f system_onlyCa.xtc -s system_onlyCa.pdb -n system_onlyCa.ndx -o
atm-pair.out
The PDB file "system_onlyCa.pdb" had a header which seems to have confused
the coun
t.peter.muel...@gmx.net wrote:
Dear Shay, dear Gromacians
For purposes of debugging this bug you can also use the flag of g_mindist
that gives out atom pairs and see which atom pairs is it that gromacs
thinks are less the 1 angstrom.
I used the "-o atm-pair.out" option to get the atom pair
Dear Peter,
For purposes of debugging this bug you can also use the flag of
g_mindist that gives out atom pairs and see which atom pairs is it
that gromacs thinks are less the 1 angstrom.
Another suggestion would be using the backbone and seeing if it matters any.
Regards,
-Shay
Quoting t
Hi,
If you use -pi with g_mindist, all the other output options are ignored.
Berk
> Date: Fri, 9 Oct 2009 14:24:00 +0200
> From: cseif...@bph.ruhr-uni-bochum.de
> To: gmx-users@gromacs.org
> Subject: [gmx-users] g_mindist
>
> Dear Mr. Gromacs, ;-)
> and hello to everybody!
>
> When I use g_mi
* Chris Neale [2009-01-17 10:11:34 -0500]:
Hello,
For my systems, I have been unable to get g_mindist -pi to function unless I
roll back to gmx 3.3.1. Would somebody please test their 4.0.2 (and perhaps
3.3.3) installations to see if the error is repeatable or perhaps is somehow
related to
Hi,
I never noticed this because I always used -s.
Supply a tpr file with -s in addition to -n and it will work.
I fixed this for 4.0.3 such that with -pi it automatically uses -s as well.
Berk
> Date: Sat, 17 Jan 2009 10:11:34 -0500
> From: chris.ne...@utoronto.ca
> To: gmx-users@gromacs.org
>
Hi Andrea,
You shouldn't fit before analysis involving PBC. Fitting changes the
orientation of the molecule with respect to the lattice. Image an
elongated molecule in a rectangular box, which rotates along its short
axis. Because of fitting, you'd miss it running into its own image...
Cheers,
Just to keep the post upgraded, I have tried:
trjconv -pbc nojump -o test.xtc
then
trjconv -fit rot+trans -f test.xtc -o test1.xtc
and then run g_mindist on test1.xtc.
The results of -pi is more or less the same that I obtain using vmd program.
Probably it might help other people with the same pro
Hi Miguel,
that's it. Visualizing the system in vmd I see that at the point the two
peptides are in two
different boxes.
I was almost sure that there were no interaction between two periodic images
from the energy
profile. In fact, the energy profile (Coul and LJ) did not show any weird
behaviou
On 6/12/2007 7:15 PM, Miguel Machuqueiro wrote:
At 08:00 AM 6/12/2007, you wrote:
Hi again,
since I did not get answer I double checked my trr file. In case I
calculate the minimum distance of
the periodic image for each component of my complex, I get reasonable
value of it (3.0 and 2.9 nm),
w
At 08:00 AM 6/12/2007, you wrote:
Hi again,
since I did not get answer I double checked my trr file. In case I
calculate the minimum distance of
the periodic image for each component of my complex, I get
reasonable value of it (3.0 and 2.9 nm),
whereas if I consider the whole system (protein) I
andrea spitaleri wrote:
Hi again,
since I did not get answer I double checked my trr file. In case I calculate
the minimum distance of
the periodic image for each component of my complex, I get reasonable value of
it (3.0 and 2.9 nm),
whereas if I consider the whole system (protein) I get this
Hi again,
since I did not get answer I double checked my trr file. In case I calculate
the minimum distance of
the periodic image for each component of my complex, I get reasonable value of
it (3.0 and 2.9 nm),
whereas if I consider the whole system (protein) I get this strange result of
0.17 nm
Hi Ozge,
'sidechain' indicates all side chains present in your system, i.e.
everything designated 'protein' based on residue names, excluding
everything taken to be 'backbone' based on atom names.
You'll probably have to run the program three times to get the
combinations of minimal distances be
mahbubeh zarrabi wrote:
Dear all
I want to analyze the electrostatic interaction in
md.I used g_mindist . in this command how can i select
distsnce for contact(-d)?
You select a value with g_mindist -d 1.0
Choosing the value is where your understanding of your scientific
problem comes in.
M
44 matches
Mail list logo
