Dear Gromacs Specialists,
I want to find information about RDF of some components in my system but when I
do the g_rdf command, I find true answers about RDF diagrams but my system type
below note in several times:
There were 2 inconsistent shifts. Check your topology
May I know that this
On 10/31/12 4:56 PM, Ali Alizadeh wrote:
Dear All users
I have a system that contains water , methane and propane in 240 k and 300
bar,
My simulation box is rectangular .
Water film is in middle of my box. Methane and propane is around it.
My simulation box is symmetric,
1- I used g_rdf
Dear Ali:
I don't think that you are re-posting the same question often enough.
Perhaps you should repost more often? 4 identical posts in 5 hours might not be
enough to get a reply
Seriously though, we all saw your message.
Chris.
-- original message(s) --
I have a system that
Dear Gromacs users
Today I encountered a new error.
I want to calculte RDF for my protein's (alpha-c) dissolved in water.
when I use the command line:
g_rdf -f traj.xtc -s topol.tpr -o rdf.xvg
and I choose 3 for (C-alpha) for both the reference and target groups, every
thing goes well and I
On 6/12/12 5:16 AM, delara aghaie wrote:
Dear Gromacs users
Today I encountered a new error.
I want to calculte RDF for my protein's (alpha-c) dissolved in water.
when I use the command line:
g_rdf -f traj.xtc -s topol.tpr -o rdf.xvg
and I choose 3 for (C-alpha) for both the reference and
Regards
D.M
From: Justin A. Lemkul jalem...@vt.edu
To: delara aghaie d_agh...@yahoo.com; Discussion list for GROMACS users
gmx-users@gromacs.org
Sent: Tuesday, 12 June 2012, 15:45
Subject: Re: [gmx-users] g_rdf (lyzozyme tutorial)
On 6/12/12 5:16 AM, delara
On 6/12/12 7:24 AM, delara aghaie wrote:
Dear Justin
I use gromacs (4.0.5).
This is the command line:
g_rdf -f md_0_1.xtc -s md_0_1.tpr -xy -o rdf.xvg
This is what appears on the screen and stops there without any change !!!
Hello,
I wish to compute rdf of Na+ ions around protein surface. I use the command:
g_rdf -f traj.xtc -n index.ndx -o rdf_prot_Na_res_com.xvg -b 4 -s md.tpr
-surf mol -rdf res_com -bin 0.01
Since when -surf option is used, g_rdf does not normalize the rdf, I am
curious what does actually
...@gromacs.org]
On Behalf Of Payman Pirzadeh
Sent: February-13-12 12:24 AM
To: 'Discussion list for GROMACS users'
Subject: RE: [gmx-users] g_rdf -surf
Hello,
Thanks for your attention. A word was missing in my previous e-mail!! The
g(r) is NOT normalized.
Here was my command:
g_rdf -f
Hello,
I am trying to calculate the RDF of water next to surface of certain
residues. I used the an index file which includes the residues as the first
group, and the #12 option (SOL) in the g_rdf, and used the option '-surf
res' on the prompt. However, the calculated RDF rises up to 41000 in
On 13/02/2012 5:54 PM, Payman Pirzadeh wrote:
Hello,
I am trying to calculate the RDF of water next to surface of certain
residues. I used the an index file which includes the residues as the
first group, and the #12 option (SOL) in the g_rdf, and used the
option '--surf res' on the prompt.
.
Sorry for inconveniences in the first iteration.
Best,
paymon
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Mark Abraham
Sent: February-13-12 12:06 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] g_rdf -surf
On 13/02/2012 5
Hi Gmx Users,
I am interested in RDF of my protein resdiues away from the given point in
a range of 10 nm. g_rdf provides mi the data for app.5 nm. Is there any
chance to change it?
Thank you
Steven
--
gmx-users mailing listgmx-users@gromacs.org
Steven Neumann wrote:
Hi Gmx Users,
I am interested in RDF of my protein resdiues away from the given point
in a range of 10 nm. g_rdf provides mi the data for app.5 nm. Is there
any chance to change it?
The range of the RDF is determined by the box size. You can use g_rdf -nopbc to
Dear Gromacs users,
I have a question related to the use of g_rdf for the calculation of
hydration of a lipid bilayer patch. I used g_rdf with -surf flag (I
tried both mol and res) and two index groups: the oxygens of waters as
first group and the atoms of the headgroups as second group. I
Would suggest you check to ensure that your index group and selection is for
the atoms you think it actually is, and visually inspect the system at a number
of times within the trajectory to see how the atoms are arranged relative to
each other (and measure some actual distances, easy to do
Dear Prof.
Thank you very much from your reply.
Best Regards
Sara
From: Dallas Warren dallas.war...@monash.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Thursday, February 2, 2012 2:49 AM
Subject: RE: [gmx-users] g_rdf
d(r) = (N
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Wednesday, February 1, 2012 2:12 AM
Subject: RE: [gmx-users] g_rdf
An RDF is normalised to the density for the entire box, so you should simply be
using that.
Catch ya,
Dr. Dallas Warren
Medicinal Chemistry and Drug Action
, every problem begins to resemble a nail.
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
Behalf Of mohammad agha
Sent: Thursday, 2 February 2012 3:48 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] g_rdf
Dear Prof.
Thank you very much from your
Dear Prof.
I am confused about generation a radial density graph (density vs distance from
center of mass), I know that I should use g_rdf. Then I count the number of
atoms in the shells around the COM of special group by trjorder -com -nshell
-r , next I use from this formula for compute
- Forwarded Message -
From: mohammad agha mra...@yahoo.com
To: gmx-users@gromacs.org gmx-users@gromacs.org
Sent: Tuesday, January 31, 2012 11:56 AM
Subject: g_rdf
Dear Prof.
I am confused about generation a radial density graph (density vs distance from
center of mass), I know
-users] g_rdf
Dear Prof.
I am confused about generation a radial density graph (density vs distance from
center of mass), I know that I should use g_rdf. Then I count the number of
atoms in the shells around the COM of special group by trjorder -com -nshell
-r , next I use from this formula
Spoel sp...@xray.bmc.uu.se
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Sunday, November 27, 2011 3:08 PM
Subject: Re: [gmx-users] g_rdf -com
On 2011-11-27 12:27, mohammad agha wrote:
Dear Prof.
I have a question about g_rdf.
I have a box consists of 500 surfactants
Dear Prof.
I have a question about g_rdf.
I have a box consists of 500 surfactants that make 10 micelle. I want to
compute rdf for surfactant relative to the center of mass of micelle.
When I do g_rdf, the program ask me 2 groups that the first one is COM, but it
is COM of molecules that I
On 2011-11-27 12:27, mohammad agha wrote:
Dear Prof.
I have a question about g_rdf.
I have a box consists of 500 surfactants that make 10 micelle. I want to
compute rdf for surfactant relative to the center of mass of micelle.
When I do g_rdf, the program ask me 2 groups that the first one is
Hello,
I run a 5ns simulation for a single glucose molecule in gas phase.
I tried to plot radial distribution function for O---H intramolecular
interactions using following command.
g_rdf -f 6.trr -s 6.tpr -n index -o
In rdf.xvg file there is no data.
Can you tell what could be the reason.
Nilesh Dhumal wrote:
Hello,
I run a 5ns simulation for a single glucose molecule in gas phase.
I tried to plot radial distribution function for O---H intramolecular
interactions using following command.
g_rdf -f 6.trr -s 6.tpr -n index -o
In rdf.xvg file there is no data.
Can you tell
Hi,
I am using gromacs_4.0.7 to calculate the Scattering Intensity as a function
of scattering vectors(q) using g_rdf -sq command .
But, I found that there is no way that one can increase/decrease the grid
spacing for structure factor calculation. I tried using -bin option , but that
does
Hi ALL,
I am using in calculating the distribution of a solvent around the COM of a
protein chain using g_rdf. When I plot the output file (attached) I get a
curve which increases first (from 1 to a value of about 2.5) and then
decreases to x-axis values ranging from 1 to 5. If I understand
Hi,
I am using gromacs_4.0.7 to calculate the Scattering Intensity as a function
of scattering vectors(q) using g_rdf -sq command .
But, I found that there is no way that one can increase/decrease the grid
spacing for structure factor calculation. I tried using -bin option , but that
does
Dear fellow Gromacs users
Does anyone know how the -surf mol option works?
I am trying to calculate the coordination number for a molecule in a slice
(xy-plane, delta-z ~ 0.5 nm) of my system. I believe I understand how to do the
integration of the RDF function if I use the center-of-mass
@gromacs.org
Date: Tue, 28 Sep 2010 16:38:58 +0800
Subject: [gmx-users] g_rdf normalization
Dear fellow Gromacs users
Does anyone know how the “–surf mol”
option works?
I am trying to calculate the coordination number for a
molecule in a slice (xy-plane, delta-z ~ 0.5 nm) of my
I would like to calculate the inter- and intra-molecular radial distribution
functions separately. I have read through g_rdf -h many times and I have a
few questions:
1. I think that I may have to modify a trp file (and not use it for the
simulations) by setting the nrexcl to the number of
Emily Curtis wrote:
I would like to calculate the inter- and intra-molecular radial
distribution functions separately. I have read through g_rdf -h many
times and I have a few questions:
1. I think that I may have to modify a trp file (and not use it for the
simulations) by setting
Hi Justin,
Thank you for your help. I will edit the topology file. I am running
GROMACS 4.0.7. I can download the latest version. The command line I was
using was:
g_rdf -n index -rdf res_com -s full -surf -o rdf08SEPT10.xvg
Emily
On Wed, Sep 8, 2010 at 5:31 PM, Emily Curtis
Emily Curtis wrote:
Hi Justin,
Thank you for your help. I will edit the topology file. I am running
GROMACS 4.0.7. I can download the latest version. The command line I
There's your problem. The -surf option only appears as of version 4.5.
was using was:
g_rdf -n index -rdf res_com
Hi,
I was trying to use g_rdf to calculate radial distribution function g(r)
between lipid tails and a peptide close to membrane. What I find is that the
g(r) never goes to 1 at long distance. It is less than 1 at long distance .
My general question is : Is it always necessary that g(r)
Hi everyone:
I am using g_rdf to calculate radial distribution function. However when I
check the memory usage using top, it seems to me that the code has a huge
memory leak. My system has 4GB memory but it usually has 40MB free memory
left after the program finishes.
Does anyone have the same
Hi Kun,
Can you tell more about what you are doing? What are you analyzing?
How large is the system? Which groups do you use for analysis. Etc.,
etc. Now, you might be right, but you might as well be jumping to
conclusions.
Cheers,
Tsjerk
On Tue, Jun 29, 2010 at 4:12 PM, Kun Huang
Dear gromacs users,
I want to calculate radial distribution function around my protein. I
want to get g_rdf for water molecules (OW) around my protein and g_rdf
for COM of some solutes around my protein. The numbers should be
averaged over all the frames. I tried to look at the mailing
pol...@fh.huji.ac.il wrote:
Dear gromacs users,
I want to calculate radial distribution function around my protein. I
want to get g_rdf for water molecules (OW) around my protein and g_rdf
for COM of some solutes around my protein. The numbers should be
averaged over all the frames. I
On Thu, Oct 22, 2009 at 05:17, Enemark Soeren ch...@nus.edu.sg wrote:
Ahh, now I understand - sorry, Omer!
No problem, glad to help.
In fact, I have compared all three single hydrogen RDFs and they are
identical and also relatively smooth. Since, however, with 3 times more data
points
Subject: Re: [gmx-users] g_rdf and number of atoms to include
On Thu, Oct 22, 2009 at 05:17, Enemark Soeren ch...@nus.edu.sg wrote:
Ahh, now I understand - sorry, Omer!
No problem, glad to help.
In fact, I have compared all three single hydrogen RDFs
On Wed, Oct 21, 2009 at 07:28, Enemark Soeren ch...@nus.edu.sg wrote:
Dear users,
I would like to compare interactions between molecules by using RDF. I have
tried looking at glycine and water, and compare the following two
interactions:
1) between the amine hydrogen atoms in glycine
...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of Omer Markovitch
Sent: Wednesday, October 21, 2009 4:27 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] g_rdf and number of atoms to include
On Wed, Oct 21, 2009 at 07:28, Enemark Soeren ch...@nus.edu.sg wrote:
Dear
Soeren
Sent: Wednesday, 21 October 2009 8:28 PM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] g_rdf and number of atoms to include
Hi Omer,
Thanks for your input.
Let me reformulate my problem:
I have glycine molecules in the form of zwitterions:
1ZGLY N
list for GROMACS users
Subject: RE: [gmx-users] g_rdf and number of atoms to include
Omar's response answered that question on why they are different. In
the first one you are grouping all three into one group, second is just
one of the hydrogen types. The fact that the rdf you get is different
be identical. Did I get that correctly?
Best regards,
Soren
*From:* gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] *On Behalf Of *Dallas B. Warren
*Sent:* Thursday, October 22, 2009 6:56 AM
*To:* Discussion list for GROMACS users
*Subject:* RE: [gmx-users] g_rdf
Dear users,
I would like to compare interactions between molecules by using RDF. I
have tried looking at glycine and water, and compare the following two
interactions:
1) between the amine hydrogen atoms in glycine and the oxygen atom
in water
2) between the carboxyl oxygen atoms
Dear gmx-users,
I simulate a vapor/water/decane/vapor interface system. The interface is xy
plane. I want to analysis water structure at the interface using g_rdf
program along z axis with -xy parameter. But the calculation is hanged as
the following:
Select a reference group and 1 group
tools which can easily do what you want.
Berk
Date: Mon, 18 May 2009 16:12:16 +0800
From: hyx...@mail.ipc.ac.cn
To: gmx-users@gromacs.org
Subject: [gmx-users] g_rdf -xy
Dear gmx-users,
I simulate a vapor/water/decane/vapor interface
system. The interface is xy plane. I want to
analysis water
Dear Berk,
I am sorry that I have a mistake in the first letter. In fact I used -bin
0.05, not 100. Yet the result is hanged. Maybe as you said, the current
Gromacs can not realize what I want to do. Thanks again!
H.Y. Xiao
___
gmx-users mailing
Hello, I am relatively new to gromacs and I really would appreciate help with
the following question.
I have used a coarse-grained model to represent a DNA fragment with
approximately 50 nm of length. I have run a Langevin dynamics simulation of DNA
with ions NA+ and CL- to study their
...@gromacs.org] On Behalf Of Pablo Umazano
Sent: Thursday, 19 March 2009 10:19 AM
To: gmx-users@gromacs.org
Subject: [gmx-users] g_rdf program
Hello, I am relatively new to gromacs and I really would
appreciate help with the following question
Hi,
When attempting to use g_rdf to calculate the structure factor for a simple
Argon liquid, I get the following error:
---
Program g_rdf_d, VERSION 3.3.3
Source code file: gmx_rdf.c, line: 622
Fatal error:
Error: atom (Ar) not in list (5
Hi,
I'm using g_rdf 3.3.3 to analyze the distribution of solvent molecules in
water. What puzzles me is that sometimes in, e.g., two sequential runs, I
get two RDF's with one of them having *uniformly* larger values than the
other. Given the fact that the RDF should in principle be normalized,
Vasilii Artyukhov wrote:
Hi everybody,
I'm dealing with aqueous solutions of some small molecules. Just to clarify:
1) When I type g_rdf, is the -com option on by default? g_rdf -h makes
me suspect it is...
read again.
2) When I type g_rdf -nocom, what point of the molecule does the
Oh yes, the -rdf option! And the run input file! That makes me feel kinda
stupid... Thank you very much sorry for the dumb questions.
But still, having read the help again, I don't quite get the logic behind
g_rdf -com -rdf atom -n -s giving me an all-zero output for the RDF between
the COM of
Ok, thanks!
2008/1/11, Berk Hess [EMAIL PROTECTED]:
Date: Fri, 11 Jan 2008 15:58:23 +0100
From: [EMAIL PROTECTED]
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] g_rdf -[no]com
Oh yes, the -rdf option! And the run input file! That makes me feel
Hi everybody,
I'm dealing with aqueous solutions of some small molecules. Just to clarify:
1) When I type g_rdf, is the -com option on by default? g_rdf -h makes me
suspect it is...
2) When I type g_rdf -nocom, what point of the molecule does the resulting
RDF correspond to?
3) g_rdf -h says
Date: Fri, 11 Jan 2008 15:58:23 +0100
From: [EMAIL PROTECTED]
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] g_rdf -[no]com
Oh yes, the -rdf option! And the run input file! That makes me feel kinda
stupid... Thank you very much sorry for the dumb
avinash kumar wrote:
Dear all,
I am having a problem in running some post analysis commands like
g_rdf on my computer . When my simulation is complete I type in the
following command to calculate the radial distribution function for the
system g_rdf -f traj.trr -s topol.tpr -o rdf.xvg -b 0
Dear all,
I am having a problem in running some post analysis commands like g_rdf on
my computer . When my simulation is complete I type in the following command
to calculate the radial distribution function for the system g_rdf -f
traj.trr -s topol.tpr -o rdf.xvg -b 0 -e 20 and the program
I compiled and installed gromacs 3.3.1 in Fedora Core 5 using gcc 4.1.0,
now,when I want to use it ,it always displays Reading frame0 time
0.000. Does anyone have the same problem with me? Is there any method
to solve the problem?
Thanks very much in advance.
root wrote:
I compiled and installed gromacs 3.3.1 in Fedora Core 5 using gcc 4.1.0,
now,when I want to use it ,it always displays Reading frame0 time
0.000. Does anyone have the same problem with me? Is there any method
to solve the problem?
Thanks very much in advance.
Osmair Vital de Oliveira wrote:
Hi Mark,
I am using GNU/Linux and when I run g_rdf appear this menssage:
'Reading frame 0 time0.000'
And nothing occur for long time...
you probably have a broken compiler. Mark asked you to specify what
installation you used. Downgrade to gcc 4.0 or
2007/3/26, syma [EMAIL PROTECTED]:
Hi,
I am attempting to calculate the rdfs of the various components of my
system
wrt to DNA phosphate groups. However, I was wondering how I can normalise
so
I can compare the various rdfs? Ideally I would like to have the g(r)
normalised in the range 0-1.
Hi,
I am attempting to calculate the rdfs of the various components of my system
wrt to DNA phosphate groups. However, I was wondering how I can normalise so
I can compare the various rdfs? Ideally I would like to have the g(r)
normalised in the range 0-1.
I have read on the user list that I
Hi,
I'm using g_rdf to calculate the RDF of a system.
The r range ends at 3nm.
I would like to change it to 100nm but it seems that there are
no option for it.
Can you help me ?
thanks,
marco
--
Marco Cammarata,
Post-Doc
European Synchrotron Radiation Facility
Material Science Group
6, rue
marco cammarata wrote:
Hi,
I'm using g_rdf to calculate the RDF of a system.
The r range ends at 3nm.
I would like to change it to 100nm but it seems that there are
no option for it.
Can you help me ?
thanks,
marco
The CVS version has an option to turn off the periodic boundary
conditions.
2007/3/7, marco cammarata [EMAIL PROTECTED]:
Hi,
I'm using g_rdf to calculate the RDF of a system.
The r range ends at 3nm.
r range ends at 3nm because (your box size)/2 is 3 nm
I would like to change it to 100nm but it seems that there are
no option for it.
100 nm? Are you sure? it
Hi all
I encounter a Fatal error:
More than 8 graph edges per atom when using g_rdf on
a trajectory that was generated using 'pbc=full'.
pbc=full circumvents this problem in mdrun. I have
seen one entry regarding this on may 2006 and
unsolved. Is there any news regarding this?
thanks
Chiradip
Hi all
I encounter a Fatal error:
More than 8 graph edges per atom when using g_rdf on
a trajectory that was generated using 'pbc=full'.
pbc=full circumvents this problem in mdrun. I have
seen one entry regarding this on may 2006 and
unsolved. Is there any news regarding this?
thanks
Chiradip
Try gmxcheck -f full.trr
How many frames are in your .trr file? Why use a .trr anyway, use the .xtc
instead (assuming that you save the xtc coords more often than the trr coords)
Next, try making an index file with make_ndx and adding -n index.ndx to your
g_rdf command. It is unclear to me how
Hi GMX ers, I posted this question earlier, but did not receive a reply. Hope to get an answer this time around.I was wondering what could be the origin of a spike at close distances when I compute the RDF of N-P atoms in a lipid bilayer system (0.25 nm) I tried using -cut option and also
Rama Gullapalli wrote:
Hi GMX ers,
I posted this question earlier, but did not receive a reply. Hope to get
an answer this time around.
I was wondering what could be the origin of a spike at close distances
when I compute the RDF of N-P atoms in a lipid bilayer system (0.25
nm) I tried
Dear All I am running a simulation of a DPPC bilayer. I am trying to compute the INTER molecular RDF s of the P-P atoms, N-P atoms and N-N atoms in the head of the bilayer. I have 2 questions,1) When I compute RDF using g_rdf, instead of a getting a smoothly decaying curve at close
Dear All I am running a simulation of a DPPC bilayer. I am trying to compute the INTER molecular RDF s of the P-P atoms, N-P atoms and N-N atoms in the head of the bilayer. I have 2 questions, 1) When I compute RDF using g_rdf, instead of a getting a smoothly decaying curve at close
Dear gromacs users,
I am using Gromacs 3.3 to simulate a coarse-grained molecule which contains
atom B and L. The atom B and L are defined myself. When the simulation
finished, I tried to use g_rdf to calculate the static structure factor. But it
gave the error message:
-
hi all
i encounter a Fatal error:
More than 4 graph edges per atom when using g_rdf on
a trajectory that was generated using 'pbc=full'.
berk hess correctly stated that pbc=full circumvents
this problem in mdrun, but i've not seen any news of
this behaviour with the analysis programs.
has
Manohar Murthi wrote:
hi all
i encounter a Fatal error:
More than 4 graph edges per atom when using g_rdf on
a trajectory that was generated using 'pbc=full'.
berk hess correctly stated that pbc=full circumvents
this problem in mdrun, but i've not seen any news of
this behaviour with the
Hi
I also have the exact same problem with g_rdf in Gromacs 3.3 and 3.3.1
on OS X 10.3.9 (segmentation fault problem). Everything else seems to
work fine. I was wandering if anyone encountered the same problem using
the same OS and how to overcome it?
Any help would be greatly appreciated
Dear friends,
I have seen a couple of postings (January 2004, gmx-developers, David
Bostick, and November 2003, gmx-users, Kay Gottschalk) on segmentation
faults from g_rdf on Mac OS X systems.
I am using the Getting Started section of the gromacs web pages, in
particular, the section on
I think we somehow fixed it in the attached version based on some
advise we found in the user list, but can't really remember the
change we made. Bad documentation. Try it out and see if it works.
Good luck,
Kay.
/*
* $Id: gmx_rdf.c,v 1.1 2004/01/25 20:37:36 lindahl Exp $
*
*
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