On 10/28/13 3:30 AM, Santu Biswas wrote:
Not working is too vague a symptom for anyone to guess what the
problem
is, sorry.
Mark
On Oct 24, 2013 9:39 AM, Santu Biswas santu.biswa...@gmail.com
wrote:
dear users,
I am performing 500ps mdrun in vacuum for
dear users,
I am performing 500ps mdrun in vacuum for polypeptide(formed
by 10-residues leucine) using gromacs_4.5.5(double-precision) using
opls-aa/L force field.Input file for 500ps mdrun is given below
title= peptide in vaccum
cpp=
Not working is too vague a symptom for anyone to guess what the problem
is, sorry.
Mark
On Oct 24, 2013 9:39 AM, Santu Biswas santu.biswa...@gmail.com wrote:
dear users,
I am performing 500ps mdrun in vacuum for polypeptide(formed
by 10-residues leucine) using
According to the suggestion I added the box to the trajectory using -box
option of trjconv, using the following commands:
trjconv -f traj.xtc -s md.tpr -box 0.9 0.9 0.9 -o traj_box.xtc
then using the g_hbond on the output trjectory (traj_box.xtc) run
successfully but gives the wrong number of
On 7/19/13 4:17 AM, bipin singh wrote:
According to the suggestion I added the box to the trajectory using -box
option of trjconv, using the following commands:
trjconv -f traj.xtc -s md.tpr -box 0.9 0.9 0.9 -o traj_box.xtc
then using the g_hbond on the output trjectory (traj_box.xtc) run
Sorry for my silly mistake.
I have a doubt regarding the expected difference in total No. of H-bonds
calculated with whole a MD trajectory (protein+solvent box) and H-bonds
calculated with concatenated frames (only protein) from a MD trajectory.
I mean, will the number of H-bonds present at a
On 7/19/13 6:55 AM, bipin singh wrote:
Sorry for my silly mistake.
I have a doubt regarding the expected difference in total No. of H-bonds
calculated with whole a MD trajectory (protein+solvent box) and H-bonds
calculated with concatenated frames (only protein) from a MD trajectory.
I
Hello all,
I was using g_hbond to calculate H-bonds for a trajectory made from several
individual snapshots from MD simulation, but because this trajectory does
not have the coordinates/information for simulation box, g_hbond is giving
the following error:
Fatal error:
Your computational box has
On 2013-07-19 06:26, bipin singh wrote:
Hello all,
I was using g_hbond to calculate H-bonds for a trajectory made from several
individual snapshots from MD simulation, but because this trajectory does
not have the coordinates/information for simulation box, g_hbond is giving
the following
Thanks a lot Prof. David. I will try this.
On Fri, Jul 19, 2013 at 10:45 AM, David van der Spoel
sp...@xray.bmc.uu.sewrote:
On 2013-07-19 06:26, bipin singh wrote:
Hello all,
I was using g_hbond to calculate H-bonds for a trajectory made from
several
individual snapshots from MD
# This file was created Fri May 24 13:03:14 2013
# by the following command:
# g_hbond -f traj_all_md.trr -s md_0_1_next1.tpr -num bovin_hnum.xvg
#
# g_hbond is part of G R O M A C S:
#
# Green Red Orange Magenta Azure Cyan Skyblue
#
@title Hydrogen Bonds
@xaxis label Time (ps)
@
Hi Maggin,
The middle column is the total number of hydrogen bonds in your system
under the definition of the hydrogen bonds criteria you have defined (here
you used the default value). The third column is the number of
acceptor-donor paris in the system. The first column is the simulation
time,
Hi,
Just to clarify: The third column are the number of acceptor-donor pairs that
fulfil the distance criterion but not the angle criterion.
Erik
On 24 May 2013, at 09:06, CHEN Pan evan.pan.c...@gmail.com wrote:
Hi Maggin,
The middle column is the total number of hydrogen bonds in your
Hello,
I am calculating the hyrogen bond life time my system using g_hbond in
Gromacs. Program calculate the hydrogen bond life time from the
autocorrelation function. Program calculate the hydrogen bond
autocorrelation function with the hydrogen bond criteria.
What quantity program use such as
On 4/14/13 7:21 PM, Nilesh Dhumal wrote:
Hello,
I am calculating the hyrogen bond life time my system using g_hbond in
Gromacs. Program calculate the hydrogen bond life time from the
autocorrelation function. Program calculate the hydrogen bond
autocorrelation function with the hydrogen bond
-ac: average over all autocorrelations of the existence functions (either
0 or 1) of all hydrogen bonds.
Program collect the data 0 or 1 along time?
nilesh
On 4/14/13 7:21 PM, Nilesh Dhumal wrote:
Hello,
I am calculating the hyrogen bond life time my system using g_hbond in
Gromacs.
On 4/14/13 8:00 PM, Nilesh Dhumal wrote:
-ac: average over all autocorrelations of the existence functions (either
0 or 1) of all hydrogen bonds.
Program collect the data 0 or 1 along time?
The presence of a hydrogen bond is a binary function. Either it exists (1) or
does not (0).
Hello,
I am calculating the hydrogen bond life time for my system, ionic liquids.
I am calculating the hydrogen bond life time using g_hbond in Groamcs.
Attached the plot p(t)vs time and the exponential decay is not sooth.
Can you tell why is there is lot of noise.
Nilesh
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Yes.
On 3 Apr 2013, at 04:07, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote:
Hello,
I am calculating the hydrogen bond life time for my system.
Do program consider the hydrogen bond criteria for calculation of
autocorrelation function?
Nilesh
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Hello,
I am calculating the hydrogen bond life time for my system.
Do program consider the hydrogen bond criteria for calculation of
autocorrelation function?
Nilesh
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To clarify: the -hbn output is not very indicative of how many
contacts there were since some of them could be present in one frame
but absent in 99. The -num option, however, provides the number of
contacts over time, and its time average probably tells you much more
in this case.
Sir,
I used gromacs 4.6. I got the point - index file will tell how many
contacts an
atom has made during the trajectory. Whether it has made a contact with an
atom only in once or all the time, in the whole trajectory, it will be
mentioned.
Am I right?
So from the problem I had, can I say that
On Mar 5, 2013, at 10:34 AM, Kavyashree M wrote:
Sir,
I used gromacs 4.6. I got the point - index file will tell how many
contacts an
atom has made during the trajectory. Whether it has made a contact
with an
atom only in once or all the time, in the whole trajectory, it will be
mentioned.
Thank you Sir.
On Tue, Mar 5, 2013 at 4:33 PM, Erik Marklund er...@xray.bmc.uu.se wrote:
On Mar 5, 2013, at 10:34 AM, Kavyashree M wrote:
Sir,
I used gromacs 4.6. I got the point - index file will tell how many
contacts an
atom has made during the trajectory. Whether it has made a
Dear users,
I used the following tool for finding the contacts
g_hbond_46 -f a.xtc -s a.tpr -contact -n a.ndx -r 0.4 -hbm a.xpm -hbn a.ndx
-num a.xvg
From the index file, the number of contacts of each atom was extracted.
This and the
xvg output was compared with another simulation.
It was found
On 3/4/13 11:25 AM, Kavyashree M wrote:
Dear users,
I used the following tool for finding the contacts
g_hbond_46 -f a.xtc -s a.tpr -contact -n a.ndx -r 0.4 -hbm a.xpm -hbn a.ndx
-num a.xvg
From the index file, the number of contacts of each atom was extracted.
This and the
xvg output was
Sir,
From Index file which gives the unique contacts -
First section the list of atoms I want to analyse
[ C_CA_CB_CD_CD1_CD2_CE_CE1_CE2_CE3_CG_CG1_CG2_CZ_CZ2_CZ3_CH2 ]
second section : the unique contacts of each atoms with others
[
On 3/4/13 12:04 PM, Kavyashree M wrote:
Sir,
From Index file which gives the unique contacts -
First section the list of atoms I want to analyse
When measuring contacts, you don't measure one group, you measure the number of
contacts that occur between groups A and B, which considers all
On Mon, Mar 4, 2013 at 11:10 PM, Justin Lemkul jalem...@vt.edu wrote:
When measuring contacts, you don't measure one group, you measure the
number of contacts that occur between groups A and B, which considers all
atoms in those two groups.
I gave a group of hydrophobic atoms in both cases
On 3/4/13 1:10 PM, Kavyashree M wrote:
On Mon, Mar 4, 2013 at 11:10 PM, Justin Lemkul jalem...@vt.edu wrote:
When measuring contacts, you don't measure one group, you measure the
number of contacts that occur between groups A and B, which considers all
atoms in those two groups.
I gave a
I am sorry There is no 7ws Its a typographic error. What I wanted to ask
was -
I am comparing two simulations S1 and S2 for contacts at a given cut off
I used g_mdmat and g_hbond to calculate it.
g_hbond outputs: of -num and -hbn was considered.
1. -hbn output was analysed to calculate
Dear users,
I have a little confusion -
The hbmap.xpm file gives the existence of each hydrogen bond.
The file mentions -
c #FF /* None */,
o c #FF /* Present */,
Meaning -
character space in white colour means Hbond not present
character o in red colour means Hbond is present.
In
On 1/24/13 11:03 AM, Kavyashree M wrote:
Dear users,
I have a little confusion -
The hbmap.xpm file gives the existence of each hydrogen bond.
The file mentions -
c #FF /* None */,
o c #FF /* Present */,
Meaning -
character space in white colour means Hbond not present
character
Thank you for the clarification.
On Fri, Jan 25, 2013 at 12:40 AM, Justin Lemkul jalem...@vt.edu wrote:
On 1/24/13 11:03 AM, Kavyashree M wrote:
Dear users,
I have a little confusion -
The hbmap.xpm file gives the existence of each hydrogen bond.
The file mentions -
c #FF /*
On 12/19/12 9:37 AM, Kavyashree M wrote:
Dear users,
While using g_hbond, does it make any difference if I give option
18 and 1 or 1 and 18?
Order does not matter.
I wanted to find the hydrogen bonding of a group of residues with
the whole protein so I had an index of this group. When I
Sir,
I thought that the order should not matter but when I used 18 - 1
and 1 - 18 the graph were slightly off.
Group 18 is a set of residues in that protein with some unique property.
I wanted to see the variation of Hbond of these residues with the whole
protein. so group 18 is a subset of
On 12/19/12 11:43 AM, Kavyashree M wrote:
Sir,
I thought that the order should not matter but when I used 18 - 1
and 1 - 18 the graph were slightly off.
Group 18 is a set of residues in that protein with some unique property.
I wanted to see the variation of Hbond of these residues with the
Ok thank you.
kavya
On Wed, Dec 19, 2012 at 10:52 PM, Justin Lemkul jalem...@vt.edu wrote:
On 12/19/12 11:43 AM, Kavyashree M wrote:
Sir,
I thought that the order should not matter but when I used 18 - 1
and 1 - 18 the graph were slightly off.
Group 18 is a set of residues in that
Dear gromacs users,
in the Gromacs manual pages (version 4.5.3 page 211) there are the
criteria to have an Hbond.
r 0.35 nm, where r is the Donor-Acceptor distance
alpha 30°, where alpha is the Hydrogen-Donor-Acceptor angle
in the Manual page for g_hbond (version 4.5.3 page 275) it is
On 11/30/12 10:41 AM, Velia Minicozzi wrote:
Dear gromacs users,
in the Gromacs manual pages (version 4.5.3 page 211) there are the criteria to
have an Hbond.
r 0.35 nm, where r is the Donor-Acceptor distance
alpha 30°, where alpha is the Hydrogen-Donor-Acceptor angle
in the Manual page
Hi
I have an alcohol system and I want to calculate the number of H bonds
during the trajectory.
My atom type labels are C2-C2-C2-CO-OH-HO. CO denotes carbon bonded to
oxygen, OH denotes alcohol oxygen, and HO denotes alcohol hydrogen.
In g_hbond how do I specify my groups to consider for H
On 9/28/12 8:53 AM, Gavin Melaugh wrote:
Hi
I have an alcohol system and I want to calculate the number of H bonds
during the trajectory.
My atom type labels are C2-C2-C2-CO-OH-HO. CO denotes carbon bonded to
oxygen, OH denotes alcohol oxygen, and HO denotes alcohol hydrogen.
In g_hbond how
Hello,
How can I add chlorin atom as a acceptor in g_hbond.
I am using Gromacs VERSION 4.0.7
NIlesh
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Nilesh Dhumal wrote:
Hello,
How can I add chlorin atom as a acceptor in g_hbond.
Either modify the source code (the search_acceptors routine in gmx_hbond.c) or
make a dummy structure/topology that lists the Cl atoms as O. The program
searches for acceptors by atom name only (O and/or N
As suggested by David I extended the simulations (total of 25ns) for a
single chain polyacid in 5500 water molecules and tried to calculate the
H-bond ACF. I get the same negative lifetime for Hbonds between COOH groups
and water. Is it that the g_hbond ACF giving weird results for this case.
For
Dear David,
Yes it is DGact.
The DGeq follows from the fraction of COOH that are not forming hydrogen
bonds, option -nhbdist.
So, I need to use the equation (9) and (10) from your paper to calculate
the equilibrium constant and free energy of H-bonding.
Another question I have is, for a
On 2011-12-12 09:54, sulatha M. S wrote:
Dear David,
Yes it is DGact.
The DGeq follows from the fraction of COOH that are not forming
hydrogen bonds, option -nhbdist.
So, I need to use the equation (9) and (10) from your paper to calculate
the equilibrium constant and free energy
I did not get a warning here. I also have simulations (20ns) of
copolyacids where again it gave me negative life time. These runs are
well equilibrated with respect to energy and Rg of the polymers. The
system is a 20 repeat unit chain in approx. 5500 water molecules. I have
done simulations
Dear gromacs users,
I did a g_hbond -ac analysis on a 10 ns trajectory of a polycarboxylate in
water. Following is the output I obtained for the polycarboxylate H-bondign
with water
ACF 36008/36008
Normalization for c(t) = 0.00709164 for gh(t) = 7.09124e-07
Hydrogen bond thermodynamics at T =
On 2011-12-12 07:41, sulatha M. S wrote:
Dear gromacs users,
I did a g_hbond -ac analysis on a 10 ns trajectory of a polycarboxylate
in water. Following is the output I obtained for the polycarboxylate
H-bondign with water
ACF 36008/36008
Normalization for c(t) = 0.00709164 for gh(t) =
Hi Gmxers,
I used g_hbond -n protein.ndx -hbn output.xvg
to get the index of all the atoms forming H-bond with the protein,
but since H-Bonds should be dynamic as time evolves, I should see changing
number of HBonds in the output.xvg which I have not seen yet.
Kinda confused.
Thanks,
Yao
Yao Yao wrote:
Hi Gmxers,
I used g_hbond -n protein.ndx -hbn output.xvg
to get the index of all the atoms forming H-bond with the protein,
but since H-Bonds should be dynamic as time evolves, I should see
changing number of HBonds in the output.xvg which I have not seen yet.
Kinda confused.
Hi Gmxers,
I ran g_hbond between my protein and water for a 3ns trajectory with 2 fs
integration step but found the error,
Cannot calculate autocorrelation of life times with less than two frames,
I am quite sure my system is just a regular protein in a cubic water box.
And the size of
Yao Yao wrote:
Hi Gmxers,
I ran g_hbond between my protein and water for a 3ns trajectory with 2
fs integration step but found the error,
Cannot calculate autocorrelation of life times with less than two frames,
I am quite sure my system is just a regular protein in a cubic water box.
And
Hi everyone!
I have some questions on g_hbond. According to Manual 4.5.4, hydrogen-bonds are
counted/determined by g_hbond based on angle and distance cut-offs. The
distance cut-off is based on the acceptor-donor distance. However, the online
manual says that the distance is based on Hydrogen
Hi everyone!
I have some questions on g_hbond. According to Manual 4.5.4, hydrogen-bonds are
counted/determined by g_hbond based on angle and distance cut-offs. The
distance cut-off is based on the acceptor-donor distance. However, the online
manual says that the distance is based on Hydrogen
Mr Bernard Ramos wrote:
Hi everyone!
I have some questions on g_hbond. According to Manual 4.5.4,
hydrogen-bonds are counted/determined by g_hbond based on angle and
distance cut-offs. The distance cut-off is based on the acceptor-donor
distance. However, the online manual says that the
Justin A. Lemkul wrote:
Mr Bernard Ramos wrote:
Hi everyone!
I have some questions on g_hbond. According to Manual 4.5.4,
hydrogen-bonds are counted/determined by g_hbond based on angle and
distance cut-offs. The distance cut-off is based on the acceptor-donor
distance. However, the
On Wed, Aug 31, 2011 at 5:54 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Steven Neumann wrote:
One question for Glycine it is easy to assess 3 possible hbonds which
can create as hydrogen is only one atom as a side chain.
How about other amino acids and their maximum hbonds they can
On 1/09/2011 6:14 PM, Steven Neumann wrote:
On Wed, Aug 31, 2011 at 5:54 PM, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu wrote:
Steven Neumann wrote:
One question for Glycine it is easy to assess 3 possible
hbonds which can create as hydrogen is only
Hi Gromacs Users,
I have calculated hydrogen bonds and collisions between my ligands and every
single residue using g_hbond. Looking at the criteria adpoted by Gromacs I
found impossible that number of hydrogen bonds were higher than number of
collisions... And what is interesting in one of my
Steven Neumann wrote:
Hi Gromacs Users,
I have calculated hydrogen bonds and collisions between my ligands and
every single residue using g_hbond. Looking at the criteria adpoted by
Gromacs I found impossible that number of hydrogen bonds were higher
than number of collisions... And what
On Wed, Aug 31, 2011 at 2:39 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Steven Neumann wrote:
Hi Gromacs Users,
I have calculated hydrogen bonds and collisions between my ligands and
every single residue using g_hbond. Looking at the criteria adpoted by
Gromacs I found impossible that
Steven Neumann wrote:
On Wed, Aug 31, 2011 at 2:39 PM, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu wrote:
Steven Neumann wrote:
Hi Gromacs Users,
I have calculated hydrogen bonds and collisions between my
ligands and every single residue using
Steven Neumann wrote:
On Wed, Aug 31, 2011 at 2:39 PM, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu wrote:
Steven Neumann wrote:
Hi Gromacs Users,
I have calculated hydrogen bonds and collisions between my
ligands and every single residue using
On Wed, Aug 31, 2011 at 3:44 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Steven Neumann wrote:
On Wed, Aug 31, 2011 at 2:39 PM, Justin A. Lemkul jalem...@vt.edumailto:
jalem...@vt.edu wrote:
Steven Neumann wrote:
Hi Gromacs Users,
I have calculated hydrogen bonds
Steven Neumann wrote:
On Wed, Aug 31, 2011 at 3:44 PM, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu wrote:
Steven Neumann wrote:
On Wed, Aug 31, 2011 at 2:39 PM, Justin A. Lemkul
jalem...@vt.edu mailto:jalem...@vt.edu
mailto:jalem...@vt.edu
Thank you for clarification Justin!!! The Manual is not as clear as you :P
Steven
On Wed, Aug 31, 2011 at 4:00 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Steven Neumann wrote:
On Wed, Aug 31, 2011 at 3:38 PM, Justin A. Lemkul jalem...@vt.edumailto:
jalem...@vt.edu wrote:
Steven
One question for Glycine it is easy to assess 3 possible hbonds which
can create as hydrogen is only one atom as a side chain.
How about other amino acids and their maximum hbonds they can create?
Steven
On Wed, Aug 31, 2011 at 4:25 PM, Steven Neumann s.neuman...@gmail.comwrote:
Thank you
Steven Neumann wrote:
One question for Glycine it is easy to assess 3 possible hbonds
which can create as hydrogen is only one atom as a side chain.
How about other amino acids and their maximum hbonds they can create?
Any OH or NH group is a donor, any lone pair is an acceptor
Hi Guys,
I am using g_hbond to analyze hbond between two groups. The manual says All
hydrogen bonds between the two groups are analyzed.
Does that mean even those hbonds do not hbond to neither of the two groups are
still under consideration?
Thanks,
Yao
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Yao Yao wrote:
Hi Guys,
I am using g_hbond to analyze hbond between two groups. The manual says
All hydrogen bonds between the two groups are analyzed.
Does that mean even those hbonds do not hbond to neither of the two
groups are still under consideration?
If it doesn't form a hydrogen
Hi,
I am little confused about setting up the two groups in g_hbond.
1. Are the two groups corresponding to the donor (N) and the acceptor (O) atoms?
I want to measure the lifetime, angle and distance of the triplet N-HO
hydrogen bond. Is this the triplet that the manual talks about?
Thanks
Hi,
To help clarify my previous g_hbond question, I have these two groups in my
index file
[ a_100_a_101] # 100 is N, #101 is H
100 101
[ a_200 ] # 200 is O
200
when I ran g_hbond, I got Found 1 donors and 2 acceptors. The part that I
don't quite understand is why it
From g_hbond -h
OH and NH groups are regarded as donors, O is an acceptor always, N
is an acceptor by default, but this can be switched using -nitacc.
Dummy hydrogen atoms are assumed to be connected to the first
preceding non-hydrogen atom.
The two groups are to find hbonds between
Hi,
I have a question related to the calculation of hydrogen bonds in Gromacs. As I
read in Manual it comes from the distance between donor and acceptor ( = 0.35
nm) and the angle =30 degr beween hydrogen and acceptor. The question is - why
30 degr? How is it related to the reality?
The
On Wed, Jun 8, 2011 at 10:20 PM, Marzinek, Jan
j.marzine...@imperial.ac.uk wrote:
Hi,
I have a question related to the calculation of hydrogen bonds in Gromacs.
As I read in Manual it comes from the distance between donor and acceptor (
= 0.35 nm) and the angle =30 degr beween hydrogen and
Marzinek, Jan wrote:
Hi,
I have a question related to the calculation of hydrogen bonds in
Gromacs. As I read in Manual it comes from the distance between donor
and acceptor ( = 0.35 nm) and the angle =30 degr beween hydrogen and
acceptor. The question is - why 30 degr? How is it
Dear all,
g_hbond of gromacs4.0.7 and 4.5.4 gives different outputs in average
hbond number. Is there any fix to g_hbond of 4.5.4? Any suggestions
are appreciated.
Bests,
Bert
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Bert wrote:
Dear all,
g_hbond of gromacs4.0.7 and 4.5.4 gives different outputs in average
hbond number. Is there any fix to g_hbond of 4.5.4? Any suggestions
are appreciated.
This is a known bug and is present (as far as I know) in all 4.5.x versions.
There is no fix yet.
-Justin
Hello gmx-users !!
I tried using g_hbond tool to analyse h-bonds on my system. I could
successfully execute the tool for two of my systems. But the third system
should the memory problem. Below I have pasted my command and its output.
*$ g_hbond -s ../md0-20.tpr -f 40-50.trr -n index_2.ndx -num
Interesting. I can't see why that wouldn't be possible in theory, but
there is a part of the code that would need rewriting, however.
Erik
Nilesh Dhumal skrev 2011-04-12 04.11:
I tried to use contact and -da together with following command
g_hbond -f 3.trr -s 3.tpr -n hbond19.ndx -nonitacc
Hello,
I am trying to calculate number of hydrogen bond (O-H---CL)in my system.
I use the following command
g_hbond -f 3.trr -s 3.tpr -n hbond18.ndx -nonitacc -num
Output file hbnum.xvg shows zero number of hydorgen bond.
Can you tell me why its showing zero no.
A strong peak is found in
Nilesh Dhumal wrote:
Hello,
I am trying to calculate number of hydrogen bond (O-H---CL)in my system.
I use the following command
g_hbond -f 3.trr -s 3.tpr -n hbond18.ndx -nonitacc -num
Output file hbnum.xvg shows zero number of hydorgen bond.
Can you tell me why its showing zero no.
A
Is there any way to specify clorin and florin atoms as a receptor.
Nilesh
On Mon, April 11, 2011 11:08 am, Justin A. Lemkul wrote:
Nilesh Dhumal wrote:
Hello,
I am trying to calculate number of hydrogen bond (O-H---CL)in my
system.
I use the following command
g_hbond -f 3.trr -s
Nilesh Dhumal wrote:
Is there any way to specify clorin and florin atoms as a receptor.
Modify the code.
-Justin
Nilesh
On Mon, April 11, 2011 11:08 am, Justin A. Lemkul wrote:
Nilesh Dhumal wrote:
Hello,
I am trying to calculate number of hydrogen bond (O-H---CL)in my
system.
I
Try the -contact option.
Erik
Nilesh Dhumal skrev 2011-04-11 17.12:
Is there any way to specify clorin and florin atoms as a receptor.
Nilesh
On Mon, April 11, 2011 11:08 am, Justin A. Lemkul wrote:
Nilesh Dhumal wrote:
Hello,
I am trying to calculate number of hydrogen bond
Is it possible to find number of hydrogen bonds using g_hbond by
considering the distance between Acceptor-hydrogen instead of the distance
between Acceptor-Donor atoms.
Nilesh
On Mon, April 11, 2011 3:32 pm, Erik Marklund wrote:
Try the -contact option.
Erik
Nilesh Dhumal skrev
When running g_hbond -h, I see the following, among other things:
-[no]da bool yes Use distance Donor-Acceptor (if TRUE) or
Hydrogen-Acceptor (FALSE)
Hope that helps.
Erik
Nilesh Dhumal skrev 2011-04-11 23.05:
Is it possible to find number of hydrogen
I tried to use contact and -da together with following command
g_hbond -f 3.trr -s 3.tpr -n hbond19.ndx -nonitacc -noda -r 0.5
-contact -num
I am getting following error.
Fatal error:Can not analyze contact between H and A: turn off -noda
Nilesh
On Mon, April 11, 2011 5:05 pm, Nilesh
@ legend length 2
@ s0 legend Hydrogen bonds
@ s1 legend Pairs within 0.35 nm
0 0 0
200 0 0
400 2 1
600 0 3
800 0 2
1000 1 0
:
Dear Justin, maybe following information helps you. When I evaluated the number of hydrogen bonds between two different groups, particularly, water and frozen atoms of the siloxane surface I got the same results with both version of GROMACS, 4.0.3 and 4.5.2.GreetingsZuzanaOn 02/15/11, Zuzana
Hi,
That suggets it's related to the new merge-on-the-fly-code and not the
pbc handling.
And it's me, not Justin, who's fixing and probably creating the bugs. :-)
Cheers,
Erik
Zuzana Benkova skrev 2011-02-16 19.58:
Dear Justin,
maybe following information helps you. When I evaluated the
Justin A. Lemkul skrev 2011-02-09 23.03:
Zuzana Benkova wrote:
Dear GROMACS users,
I have used g_hbond of version 4.5.2 to analyze number of hydrogen
bonds in water. I got the average number per time frame and number
of water oxygen atoms equal to 0.839. When I used g_hbond of version
Hello Justin, I was using cubic boxes. GreetingsZuzanaOn 02/15/11, Erik Marklund er...@xray.bmc.uu.se wrote:Justin A. Lemkul skrev 2011-02-09 23.03:Zuzana Benkova wrote:Dear GROMACS users,I have used g_hbond of version 4.5.2 to analyze number of hydrogen bonds in water. I got the average number
Dear GROMACS users,I have used g_hbond of version 4.5.2 to analyze number of hydrogen bonds in water. I got the average number per time frame and number of water oxygen atoms equal to 0.839. When I used g_hbond of version 4.0.7 I got 1.677, which is twice the former value. TIP3P model predicts
Zuzana Benkova wrote:
Dear GROMACS users,
I have used g_hbond of version 4.5.2 to analyze number of hydrogen bonds
in water. I got the average number per time frame and number of water
oxygen atoms equal to 0.839. When I used g_hbond of version 4.0.7 I got
1.677, which is twice the former
Hi All:
Has there been further resolution on the difference between g_hbond in v 4.0 and
4.5 (I'm running 4.5.3)? For counting water-water (tip4p) h-bonds in a box of
506 waters I get the following nhbdist output, which appears to neglect pbc
since there are such a large number of unbound donor-H
Hi,
No. But I hope to get it done this week. Thanks for the reminder.
Erik
Robin C. Underwood skrev 2010-12-05 19.19:
Hi All:
Has there been further resolution on the difference between g_hbond in v 4.0 and
4.5 (I'm running 4.5.3)? For counting water-water (tip4p) h-bonds in a box of
506
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 file? which of them is more suitable for HB
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