shahab shariati skrev 2010-11-24 16.24:
Dear gromacs users
I used g_hbond -f .trr -s .tpr -n .ndx -ac -life.
Can anyone clarify last 2 columns in hblife.xvg and last 4 columns
hbac.xvg
files by details. Also, I want to know what is difference between p(t)
in hblife.xvg and c(t) in
hbac.xvg
Dear Erik
thanks.
thus -ac is only for determine the rate for hb breaking. is it true? or
there is other usable case for -ac option?
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shahab shariati skrev 2010-11-24 16.45:
Dear Erik
thanks.
thus -ac is only for determine the rate for hb breaking. is it true?
or there is other usable case for -ac option?
And formation. And equillibrium constant.
--
---
Erik Marklund, PhD
Hi Carla,
I've seen this behavior too but I didn't look at the code. I figured with
the hydrogen included it checks the angle too or if the hydrogen is between
the two heavy atoms. So the first pass just looks at distances between donor
and acceptor atoms and doesn't consider that the hydrogen
Hi,
I'm thinking it *may* have something to do with how search_donors() and
the -merge flag work. The hydrogen must be part of the index group you
provide. Nothing strange there. But the hydrogen that is printed to the
index file may in fact *not* be the hydrogen bonding one if the -merge
Hi,
I have looked at the files to sent me, and I can't spot any errors.
There *is* a hydrogen bond at y=1. It only occurs in 5 frames though, so
they're really hard to find when isnpecting the xpm in e.g. Gimp, since
the image is 6 pixels wide. So, I got tired of sqinting in front of
Dear Erik
Thanks for your attention.
What is your mean of [but keep in mind that the matrix is displayed with the
first row at the bottom].
Please clarify that more.
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Please search the
Dear gromacs users
I used g_hbond -f *.xtc -s *.tpr -n *.ndx -hbm hbmap.xpm for hydrogen bond
analysis.
then I used xpm2ps -f hbmap.xpm -o hbmap.eps.the ps file is hydrogen bond
index vs time. I don't understand numbers in vertical axis. do these numbers
in vertical axis relate to hbond.ndx
shahab shariati wrote:
Dear Erik
Thanks for your attention.
What is your mean of [but keep in mind that the matrix is displayed with
the first row at the bottom].
Please clarify that more.
The last line of the .xpm file corresponds to the first entry in the H-bonds
section of
Dear Erik and Justin
Thanks for your time and attention.
My xpm file is following state:
/* XPM
*/
/* Generated by g_hbond
*/
/* This file can be converted to EPS by the GROMACS program xpm2ps
*/
/* title: Hydrogen Bond Existence Map
*/
/* legend: Hydrogen Bonds
*/
/* x-label: Time (ps)
shahab shariati wrote:
Dear Erik and Justin
Thanks for your time and attention.
My xpm file is following state:
/* XPM
*/
/* Generated by g_hbond
*/
Dear Justin
Thus, if there are 40 hydrogen bond. Numerical indice 5 on the y-axis of
.eps file is same to indice 35 in .ndx file. Is it true?
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shahab shariati wrote:
Dear Justin
Thus, if there are 40 hydrogen bond. Numerical indice 5 on the y-axis of
.eps file is same to indice 35 in .ndx file. Is it true?
No. Index 5 of the .ndx file corresponds to data line 35 of the .xpm file. The
output .eps file is numbered in
Hi everyone,
I ran g_hbond on a trajectory. When g_hbond asks for two groups in the index
file, I give:
group1: Protein
group2: ligand
The output .ndx file contains 44 Hbonds.
In order to verify my result on each and every Hbond, I ran g_hbond on the
same trajectory but this time in my index
...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of shahab shariati
Sent: Tuesday, 9 November 2010 5:35 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] g_hbond / lifetime
Dear Dallas Warren
Thanks for your attention.
Thus, if I select a certain hydrogen bond from *.ndx file, g_hbond
Dear all
I used g_hbond for analysis of hydrogen bonds between protein-ligand
complex.
g_hbond -f *.xtc -s *.tpr -n *.ndx -num -g -ac -dist -ang -hx -hbn -hbm -don
-dan -life -nhbdist
after using g_hbond, gromacs gives me: HB lifetime = 16.82 ps
this lifetime is related with what hydrogen
I would like to modify the g_hbond code (or preferably, know how to implement
g_hbond if it is already capable) to count the number of non-hydrogen bound
water OH donors in a simulation. I define a non-hydrogen bound donor as one that
does not meet the distance requirement, or one that may meet
Robin C. Underwood wrote:
I would like to modify the g_hbond code (or preferably, know how to implement
g_hbond if it is already capable) to count the number of non-hydrogen bound
water OH donors in a simulation. I define a non-hydrogen bound donor as one that
does not meet the distance
Dear Dallas Warren
Thanks for your attention.
Thus, if I select a certain hydrogen bond from *.ndx file, g_hbond give me
HB lifetime only for that certain hydrogen bond. Is it true?
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Please
Hi Erik,
I tried what you said: I made index groups containing only the atoms
involved in that hbond and ran g_hbond again. The problem didn't persist.
So I wanted to check if I misinterpreted the map: for that, I compared my 4
index files: the one of my concatenated trajectory and the three of
Hi,
Let me have a look at the files off-list and I'll probably see what's
going on.
Erik
Carla Jamous skrev 2010-11-04 11.32:
Hi Erik,
I tried what you said: I made index groups containing only the atoms
involved in that hbond and ran g_hbond again. The problem didn't persist.
So I wanted
Hi to all,
I'm sorry I'm asking again a question I asked a week ago but I still haven't
found my answer:
I concatenated 3 trajectories of 3 different molecules (that have the same
number of atoms) with trjcat: trjcat -settime
Then I ran g_hbond on the concatenated trajectory, I got an index.ndx
Carla Jamous skrev 2010-11-02 17.35:
Hi to all,
I'm sorry I'm asking again a question I asked a week ago but I still
haven't found my answer:
I concatenated 3 trajectories of 3 different molecules (that have the
same number of atoms) with trjcat: trjcat -settime
Then I ran g_hbond on the
Erik Marklund skrev 2010-11-02 20.33:
Carla Jamous skrev 2010-11-02 17.35:
Hi to all,
I'm sorry I'm asking again a question I asked a week ago but I still
haven't found my answer:
I concatenated 3 trajectories of 3 different molecules (that have the
same number of atoms) with trjcat:
Hi everyone,
please I need some help on g_hbond.
I concatenated 3 trajectories. I ran g_hbond on the concatenated trajectory.
I got the result of h_bonds.
Then I wanted to run g_hbond on each of my 3 trajectories. Here, I get a
different result, it means: if I take the first 10ps of my
Carla Jamous skrev 2010-10-15 12.05:
Hi everyone,
please I need some help on g_hbond.
I concatenated 3 trajectories. I ran g_hbond on the concatenated
trajectory. I got the result of h_bonds.
Then I wanted to run g_hbond on each of my 3 trajectories. Here, I get
a different result, it
No, I don't think so because I did an .eps file (with xpm2ps) that indicates
the Time(ps) in x-axis and Hydrogen Bond Index in y-axis.
This is the way I'm reading my matrix.
Carla
On Fri, Oct 15, 2010 at 12:09 PM, Erik Marklund er...@xray.bmc.uu.sewrote:
Carla Jamous skrev 2010-10-15 12.05:
Yes, and it's the y-direction that is tricky. If I'm not mistaken, the
first row in the matrix is the *bottom* line in the graphical output.
Thus, the bottom line in the picture would be the first hbond in the
corresponding index file.
Erik
Carla Jamous skrev 2010-10-15 12.12:
No, I don't
Carla Jamous skrev 2010-10-15 12.05:
Hi everyone,
please I need some help on g_hbond.
I concatenated 3 trajectories. I ran g_hbond on the concatenated
trajectory. I got the result of h_bonds.
Then I wanted to run g_hbond on each of my 3 trajectories. Here, I get
a different result, it
I'm sorry I don't understand, because your last answer doesn't correspond to
what's written in the manual. I'm using gromacs 4.0.3 and the manual says:
-hbm: existence matrix. Ordering is identical to that in -hbn index file.
And yes, my trajectory is concatenated the way I intended to, but I
The tricky part is that if you look at the first line in the file
hbm.xpm you are looking at the bottom row of the matrix when displayed
with gimp or after converting to xpm2ps. The same line corresponds to
the first hbond in hbn.ndx. That sentence in the manual is therefore a
bit ambiguous.
Has anybody checked g_hbond results for consistency between v4.0.7 and v4.5.1?
My usage is:
g_hbond -f my.xtc -r 0.68 -contact -life -s my.tpr -ac
and I find that the output files hbnum.xvg, hbac.xvg, hblife.xvg, and
the ac-reported lifetime of interactions are all different. To show
the
If I redo this, selecting only a single acceptor atom and 64 donor
atoms, with a large cutoff distance of 3 nm, v4.0.7 gives me 44
should have read 4 nm above. the point is that there really are 44
contacts, but v4.5.1 reports only 1.
contacts in one frame while v4.5.1 gives me only 1
chris.ne...@utoronto.ca skrev 2010-10-15 16.58:
If I redo this, selecting only a single acceptor atom and 64 donor
atoms, with a large cutoff distance of 3 nm, v4.0.7 gives me 44
should have read 4 nm above. the point is that there really are 44
contacts, but v4.5.1 reports only 1.
someone can help me.
Many thanks,
Yao
--- On Wed, 9/29/10, Erik Marklund er...@xray.bmc.uu.se wrote:
From: Erik Marklund er...@xray.bmc.uu.se
Subject: Re: [gmx-users] g_hbond segmentation fault
To: Discussion list for GROMACS users gmx-users@gromacs.org
Date: Wednesday, September 29
?to=er...@xray.bmc.uu.se
Subject: Re: [gmx-users] g_hbond segmentation fault
To: Discussion list for GROMACS users gmx-users@gromacs.org
/mc/compose?to=gmx-us...@gromacs.org
Date: Wednesday, September 29, 2010, 7:55 AM
Hi Gmxers,
I used the command line,
g_hbond -f tst.trr -s tst.tpr -ac test -e 500 -dt 1
and I got the message like,
--
Found 1048 different hydrogen bonds in trajectory
Found 2292 different atom-pairs within hydrogen bonding distance
Merging hbonds with Acceptor
van der Spoel /sp...@xray.bmc.uu.se/* wrote:
From: David van der Spoel sp...@xray.bmc.uu.se
Subject: Re: [gmx-users] g_hbond segmentation fault
To: Discussion list for GROMACS users gmx-users@gromacs.org
Date: Wednesday, September 29, 2010, 6:11 AM
On 2010-09-29 08.02, Yao Yao
--
Found 1048 different hydrogen bonds in trajectory
Found 2292 different atom-pairs within hydrogen bonding distance
Merging hbonds with Acceptor and Donor swapped
2/10915Segmentation fault
__
Hi guys,
I got the msg like above when
Yao Yao skrev 2010-09-27 21.22:
--
Found 1048 different hydrogen bonds in trajectory
Found 2292 different atom-pairs within hydrogen bonding distance
Merging hbonds with Acceptor and Donor swapped
2/10915Segmentation fault
__
Hi
hello,
I have a trajectory generated by gromacs in which I excluded water and
there is only protein, now I like to see how does the number of h_bond
between water and protein change during the trajectory. In fact when I
use g_hbond I can choose the water and protein but I was wondering where
Fahimeh Baftizadeh Baghal wrote:
hello,
I have a trajectory generated by gromacs in which I excluded water and
there is only protein, now I like to see how does the number of h_bond
between water and protein change during the trajectory. In fact when I
use g_hbond I can choose the water and
On 9/17/10 5:37 PM, Justin A. Lemkul wrote:
Fahimeh Baftizadeh Baghal wrote:
hello,
I have a trajectory generated by gromacs in which I excluded water and
there is only protein, now I like to see how does the number of h_bond
between water and protein change during the trajectory. In fact
that ...
Anyway since I have gro files time to time, I think I will cat all the gro file
and use that for analysis of h_bond.
Fahimeh
--- On Fri, 9/17/10, David van der Spoel sp...@xray.bmc.uu.se wrote:
From: David van der Spoel sp...@xray.bmc.uu.se
Subject: Re: [gmx-users] g_hbond
Justin A. Lemkul skrev 2010-09-10 22.33:
ceste...@unsl.edu.ar wrote:
Hi all:
I´m using gromacs version 4.0.2 and a box type truncated octahedron for
the MD simulation.
I need to analyze hydrogen bonds with solvent (water)insertion.
I used the following command:
g_hbond –f *.xtc –s *.tpr –n
Hi all:
I´m using gromacs version 4.0.2 and a box type truncated octahedron for
the MD simulation.
I need to analyze hydrogen bonds with solvent (water)insertion.
I used the following command:
g_hbond f *.xtc s *.tpr n *.ndx num num.xvg dist *.xvg ang *.xvg a
45 r 0.3 ins.
I selected
Nilesh Dhumal wrote:
THanks.
I have one more system dioxin + water molecules. There is possiblity of
C-H---O hydrogen bond. The CH bond of dioxin and oxygen atom of water.
I want to calculate the number of hydrogen bonds.
I used the following command
g_hbond -f dix-bdmp.trr -s dix-bdmp.tpr
Justin A. Lemkul skrev 2010-08-31 12.35:
Nilesh Dhumal wrote:
THanks.
I have one more system dioxin + water molecules. There is possiblity of
C-H---O hydrogen bond. The CH bond of dioxin and oxygen atom of water.
I want to calculate the number of hydrogen bonds.
I used the following command
Hello,
I have a system with a glucose molecule and 256 water molecules.
I want to find out the number of hydrogen bond between the hydrogen atom
of OH group of glucose and the oxygen atom of water.
How can I make the index file.
Thanks
NIlesh
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gmx-users mailing list
Nilesh Dhumal wrote:
Hello,
I have a system with a glucose molecule and 256 water molecules.
I want to find out the number of hydrogen bond between the hydrogen atom
of OH group of glucose and the oxygen atom of water.
How can I make the index file.
Type help at the make_ndx prompt for
- Original Message -
From: Nilesh Dhumal ndhu...@andrew.cmu.edu
Date: Tuesday, August 31, 2010 12:42
Subject: [gmx-users] g_hbond
To: gmx-users@gromacs.org
Hello,
I have a system with a glucose molecule and 256 water molecules.
I want to find out the number of hydrogen bond between
THanks.
I have one more system dioxin + water molecules. There is possiblity of
C-H---O hydrogen bond. The CH bond of dioxin and oxygen atom of water.
I want to calculate the number of hydrogen bonds.
I used the following command
g_hbond -f dix-bdmp.trr -s dix-bdmp.tpr -n dix-bdmp-no.ndx -num
I
Below is the hbond.xvg content 1 coloumn is for time second for numbers,
but I am not getting for 3rd one i.e. Pairs within 0.35 nm is this shows
area in cutoff range?
@ title Hydrogen Bonds
@ xaxis label Time
@ yaxis label Number
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend
pawan raghav wrote:
Below is the hbond.xvg content 1 coloumn is for time second for numbers,
but I am not getting for 3rd one i.e. Pairs within 0.35 nm is this shows
area in cutoff range?
Search the mailing list archive. I answered this identical question last week.
If you use the
hi out there,
still doing my first steps on the gmx planet. can anyone tell me, why
there are 3 columns in the output file of g_hbond and how to interpret
the output values when having run
g_hbond -f mdNew.xtc -s md.tpr -num mdNew_numH.xvg
first column frame!
second column = #H bonds?
third
On 2010-03-17 16.26, vedat durmaz wrote:
hi out there,
still doing my first steps on the gmx planet. can anyone tell me, why
there are 3 columns in the output file of g_hbond and how to interpret
the output values when having run
g_hbond -f mdNew.xtc -s md.tpr -num mdNew_numH.xvg
first column
I used g_hbond for analysis of hydrogen bonds.
g_hbond -f *.xtc -s *.tpr -n *.ndx -num -g -ac -dist -ang -hx -hbn -hbm -don
-dan -life -nhbdist -a 30 -r 0.35
Following text was turned up:
ACF 288/288
Normalization for c(t) = 0.0204067 for gh(t) = 8.10294e-06
WARNING: Correlation
On 2010-03-13 09.40, shahab shariati wrote:
I used g_hbond for analysis of hydrogen bonds.
g_hbond -f *.xtc -s *.tpr -n *.ndx -num -g -ac -dist -ang -hx -hbn -hbm
-don -dan -life -nhbdist -a 30 -r 0.35
Following text was turned up:
ACF 288/288
Normalization for c(t) = 0.0204067 for gh(t) =
Hi
I used g_hbond for analyzing hydrogen bonds.
What is difference between [s0 legend Ac\sfin sys\v{}\z{}(t)] and [s1 legend
Ac(t)] in hbac.xvg file in below?
@title Hydrogen Bond Autocorrelation
@xaxis label Time (ps)
@yaxis label C(t)
@ s0 legend Ac\sfin sys\v{}\z{}(t)
@
On 2/22/10 9:47 AM, leilakar...@aol.com wrote:
Hi
I used g_hbond for analyzing hydrogen bonds.
What is difference between [s0 legend Ac\sfin sys\v{}\z{}(t)] and [s1
legend Ac(t)] in hbac.xvg file in below?
First one is corrected for the fact that in a finite system the ACF
does not go to
Dear all,
Does any know why g_hbond does not (at least in a straightforward way)
enable the calculation of hbonds involving sulfur atoms (e.g. between
cysteines and other residues)? Is there an easy way to tell gromacs to
consider sulfur a donor and acceptor atom?
Thanks in advance
Diana Lousa
Diana Lousa wrote:
Dear all,
Does any know why g_hbond does not (at least in a straightforward way)
enable the calculation of hbonds involving sulfur atoms (e.g. between
cysteines and other residues)? Is there an easy way to tell gromacs to
consider sulfur a donor and acceptor atom?
The
Diana Lousa
Protein Modelling Laboratory
Instituto de Tecnologia Química e Biológica
Universidade Nova de Lisboa
Portugal
On Thu, 15 Oct 2009, Justin A. Lemkul wrote:
Diana Lousa wrote:
Dear all,
Does any know why g_hbond does not (at least in a straightforward way)
enable the
Hi Diana,
Well, minorities should not be disregarded just because they are poorly
represented...In some cases a rare event makes all the difference. I think
it would be helpeful to have the possiblity to calculate S-H...X bonds or
X-H...S bonds with g_hbond.
In many cases these tools come
David van der Spoel wrote:
Alvaro Cortes wrote:
Hi all.
I'm new at the list so i don't know if something similar has been
discussed before.
I tried to search in the archives, but i can't find something similar.
I have a doubt about g_hbond and fluor acceptors. As i can see in the
code, no
Alvaro Cortes wrote:
Hi all.
I'm new at the list so i don't know if something similar has been
discussed before.
I tried to search in the archives, but i can't find something similar.
I have a doubt about g_hbond and fluor acceptors. As i can see in the
code, no parsing of F atoms is done in
Dear Gmx Users,
I need to calculate the H-Bonds of simulation trajectory with specification
of i to i+2/3/4/5 so on..and i to i -2/3/4/5 so on...separately.
Do anyone have any idea how to do this...since the present option g_hbond
calculate both the hydrogen bonds together irrespective of i to
Anil Kumar wrote:
Dear Gmx Users,
I need to calculate the H-Bonds of simulation trajectory with specification
of i to i+2/3/4/5 so on..and i to i -2/3/4/5 so on...separately.
Do anyone have any idea how to do this...since the present option g_hbond
calculate both the hydrogen bonds together
Anil Kumar wrote:
Dear Mark,
Thanks for your suggestions of including/using index file. This is fine
but is it not a cumbersome process to define for different length of
systems in this way! Since, one has to define/make the group for each
carbonyl group with other pairs!
Using index
Justin A. Lemkul skrev:
krishnakumar wrote:
Hi,
Has any one encountered this error while using g_hbond?
*
Select a group: 12
Selected 12: 'SOL'
Select a group: 12
Selected 12: 'SOL'
Calculating hydrogen bonds in SOL (20949
Hi,
Has any one encountered this error while using g_hbond?
*
Select a group: 12
Selected 12: 'SOL'
Select a group: 12
Selected 12: 'SOL'
Calculating hydrogen bonds in SOL (20949 atoms)
krishnakumar wrote:
Hi,
Has any one encountered this error while using g_hbond?
*
Select a group: 12
Selected 12: 'SOL'
Select a group: 12
Selected 12: 'SOL'
Calculating hydrogen bonds in SOL (20949 atoms)
Dear GROMACS Users,
I'm trying to use g_hbond (v4.0.3) to analyze a simulation which was
generated with NAMD (trajectory was converted to .trr w/VMD). The
g_hbond requires (i) a trajectory file, and (ii) a 'run input file'
(tpr/tpa/tpb). How do i generate this tpr/tpa/tpb file? Is there any
way
Dmitry Lupyan wrote:
Dear GROMACS Users,
I'm trying to use g_hbond (v4.0.3) to analyze a simulation which was
generated with NAMD (trajectory was converted to .trr w/VMD). The
g_hbond requires (i) a trajectory file, and (ii) a 'run input file'
(tpr/tpa/tpb). How do i generate this
Dmitry Lupyan wrote:
Dear GROMACS Users,
I'm trying to use g_hbond (v4.0.3) to analyze a simulation which was
generated with NAMD (trajectory was converted to .trr w/VMD). The
g_hbond requires (i) a trajectory file, and (ii) a 'run input file'
(tpr/tpa/tpb). How do i generate this tpr/tpa/tpb
At the risk of exposing my density in triangle geometry here, why does 180-DHA
= ADH?
H
/ \
D - A
Thank you.
-Rob
Obviously the DHA angle in a linear Hbond is
180, so it should either be 180-DHA or ADH. The ADH angle is what's
implemented in gromacs 3.2.1, however in
rob yang wrote:
At the risk of exposing my density in triangle geometry here, why does
180-DHA = ADH?
H
/ \
D - A
This shows it... I confused it even further. The angle we have been
using since 3.2 is HDA. If 0, it is perfect, if more than 30 (-acut
option) it is not
...@xray.bmc.uu.se
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] g_hbond angle def
rob yang wrote:
At the risk of exposing my density in triangle geometry here, why does
180-DHA = ADH?
H
/ \
D - A
This shows it... I confused it even further. The angle we have been
Hi list,
What's the geometric relation b/w the commonly used Donor-H-Acceptor angle and
the gromacs implementation of Acceptor-Donor-H angle? I guess I don't quite
follow why it's valid to define the ADH cutoff as 30 degrees, the same angle
most commonly used to define DHA, which suggests
rob yang wrote:
Hi list,
What's the geometric relation b/w the commonly used Donor-H-Acceptor
angle and the gromacs implementation of Acceptor-Donor-H angle? I guess
I don't quite follow why it's valid to define the ADH cutoff as 30
degrees, the same angle most commonly used to define DHA,
Dear Gromacs users,
I am trying to analyze hydrogen bonding between a Protein and Drug by
g_hbond from .xtc and .tpr and .ndx files. I am getting expected results
when the H-bond donor and the hydrogen atom is from protein while the
hydrogen bond acceptor atom is in the drug. The results are,
geeta kant wrote:
Dear Gromacs users,
I am trying to analyze hydrogen bonding between a Protein and Drug by
g_hbond from .xtc and .tpr and .ndx files. I am getting expected results
when the H-bond donor and the hydrogen atom is from protein while the
hydrogen bond acceptor atom is in the
Mark Abraham wrote:
geeta kant wrote:
Dear Gromacs users,
I am trying to analyze hydrogen bonding between a Protein and Drug by
g_hbond from .xtc and .tpr and .ndx files. I am getting expected
results when the H-bond donor and the hydrogen atom is from protein
while the hydrogen bond
Dear users,
I computed the hydrogen bonds between solvent and protein in a 200 ps fraction
of a MD trajectory
with g_hbond in two different ways:
in a single step with the command:
g_hbond -b 400 -e 600 -hbn -hbm -g 400_600.log -num -n file.ndx -s file.tpr -f
file.xtc
in four steps with the
Jean-Paul Becker wrote:
Dear users,
I computed the hydrogen bonds between solvent and protein in a 200 ps fraction
of a MD trajectory
with g_hbond in two different ways:
in a single step with the command:
g_hbond -b 400 -e 600 -hbn -hbm -g 400_600.log -num -n file.ndx -s file.tpr -f
file.xtc
Hi Nicolas,
1. Does g_hbond takes into account the periodic boundary conditions
or should first I center the system on my molecule, then run g_hbond?
Yes (pretty much all tools do).
2. When I run g_hbond, it prints the message No option -sel the
usual welcome message and run
Hi all,
I have issued the command of g_hbond like this
g_hbond -f .xtc -s .tpr -n .ndx -num .xvg -hbm.map -a 30
while finishing of this command, it told 1 H-bond found and run successfully.
When I plotted .xvg file by using gnuplot its showed zigzag manner
graph(abnormal) and I never got this
minnale wrote:
Hi all,
I have issued the command of g_hbond like this
g_hbond -f .xtc -s .tpr -n .ndx -num .xvg -hbm.map -a 30
while finishing of this command, it told 1 H-bond found and run
successfully. When I plotted .xvg file by using gnuplot its showed
zigzag manner graph(abnormal) and
Thanks Justin for your response
you are telling that whatever generated output .xvg files of two systems from
g_hbond is perfect. But when I plot .xvg files with help of xmgrace it
depicting hydrogen bonds represents at bottom and contact pairs above in one
plot(one system).I am sending file
minnale wrote:
Thanks Justin for your response
you are telling that whatever generated output .xvg files of two systems
from g_hbond is perfect. But when I plot .xvg files with help of
xmgrace it depicting hydrogen bonds represents at bottom and contact
pairs above in one plot(one system).I
minnale wrote:
Thanks Justin for your reply
I am interested to get file which contain how many hydrogen bonds are
there in my protein and the bonds present between which atoms?
Is there anyway to get this file
can you please tell me,
g_hbond -h
Thanks in advance for your kind suggestion
Hi all,
I am new to gromacs, I am interested in calculate Hydrogen bonds of my
protein. So I have issued the *g_hbond command like this
g_hbond -f .xtc -s .tpr -n .ndx(Index file contain all residues mainchain+H
atoms) -num .xvg -g .log
its showed
Program g_hbond, VERSION 3.3.1
Source
minnale wrote:
Hi all,
I am new to gromacs, I am interested in calculate Hydrogen bonds of my
protein. So I have issued the *g_hbond command like this
g_hbond -f .xtc -s .tpr -n .ndx(Index file contain all residues
mainchain+H atoms) -num .xvg -g .log
its showed
Program g_hbond, VERSION
Thanks Justin for your quick reply
the g_hbond command ran succesfully and gave me .xvg file and it contain 3
columns
that is like
@title Hydrogen Bonds
@xaxis label Time
@yaxis label Number
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype
Thanks Justin for your quick reply
the g_hbond command ran succesfully and gave me .xvg file and it contain 3
columns
that is like
@title Hydrogen Bonds
@xaxis label Time
@yaxis label Number
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype
minnale wrote:
Thanks Justin for your quick reply
the g_hbond command ran succesfully and gave me .xvg file and it contain
3 columns
that is like
@title Hydrogen Bonds
@xaxis label Time
@yaxis label Number
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@
Thanks Justin for your reply
I am interested to get file which contain how many hydrogen bonds are there in
my protein and the bonds present between which atoms?
Is there anyway to get this file
can you please tell me,
Thanks in advance for your kind suggestion
On Thu, 28 Aug 2008 Justin
[EMAIL PROTECTED] wrote:
Message: 1
Date: Tue, 26 Aug 2008 15:38:56 +0530 (IST)
From: [EMAIL PROTECTED]
Subject: [gmx-users] g_hbond output analysis
To: gmx-users@gromacs.org
Message-ID: [EMAIL PROTECTED]
Content-Type: text/plain;charset=iso-8859-1
hi
i used the -num option for g_hbond run
hi
i used the -num option for g_hbond run. since i new to gromacs i cannot
able to interpret the output form. it comes in 3 columns with the first
column indicating the frame, i dont know about the remaining two columns
Kindly suggest
Parthiban sundar
Hi,
On Tuesday, 26. August 2008, [EMAIL PROTECTED] wrote:
hi
i used the -num option for g_hbond run. since i new to gromacs i cannot
able to interpret the output form. it comes in 3 columns with the first
column indicating the frame, i dont know about the remaining two columns
if you use
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