Hi users/developers,
I identified 2 issues in the center_coords function of g_density that make
the flag -center incorrectly center the system. These are in addition to
the issues previously raised by Chris Neale (reported as issue 1168 on
redmine: http://redmine.gromacs.org/issues/1168). I have a
On Tue, Apr 2, 2013 at 12:53 PM, Elisabeth wrote:
> Hi Justin,
>
> Do I have to read less frames to circumvent the problem? I know g_density
> has been used for this purpose so there should be a way to resolve this. I
> am reading 1000 frames...
>
>
1000 frames shouldn't be a problem, but it's an
Hi Justin,
Do I have to read less frames to circumvent the problem? I know g_density
has been used for this purpose so there should be a way to resolve this. I
am reading 1000 frames...
Thanks
On 2 April 2013 12:40, Justin Lemkul wrote:
>
>
> On 4/2/13 11:57 AM, Elisabeth wrote:
>
>> Dear all
On 4/2/13 11:57 AM, Elisabeth wrote:
Dear all,
I am trying to get the density profile for my liquid-vacuum interface using
g_density -f trr -s tpr however g_density gives Segmentation fault. Does
anyone had clue what could be wrong? Please comment, Thanks.
Group 0 ( System) has X
Dear all,
I am trying to get the density profile for my liquid-vacuum interface using
g_density -f trr -s tpr however g_density gives Segmentation fault. Does
anyone had clue what could be wrong? Please comment, Thanks.
Group 0 ( System) has XXX elements
Group 1 ( Other)
What output do you get from gmxcheck -f martin_md_290K_100ns_tau1.xtc ? Also,
can you extract that problematic frame with trjconv and run g_density on that
one frame (what happens?). Also, can you make a new .xtc that is missing that
last frame and see what g_density does?
These will help you t
Hi All
I have a 100 ns lipid simulation for which I want the density profile. I
issued the following command
g_density -f martin_md_290K_100ns_tau1.xtc -n dppc.ndx -s
martin_md_290K_100ns_tau1.tpr -o water_density.xvg -b 5
The program fails with the following message
Selected 3: 'Water'
Last
Dear Ali:
I assure you that all relevant information has been provided. As I said, it's
not simple. If it is beyond your
abilities then perhaps you should find a local collaborator. These days, many
computational consortia have
computational specialists who can help you with your scripting and
On 10/16/12 7:55 AM, Ali Alizadeh wrote:
Dear All users
1- When i use these commands for generating number density profile
I see completely different results(in z direction, length in z
direction is 8, number density versus of z)
g_density -f md.xtc -s md.tpr -dens number -o dens8.xvg -d z
Dear Matthias:
Did you run trjconv -center -pbc mol at some point before running
g_density? With pbc, there are multiple ways to put the center of a
system at the center of the box. This can lead to having the water
slab in the center of the unit cell and the bilayer on the top and
bottom
Hi,
I have aligned a trajectory to a reference structure and have now run
g_density on both the original and the aligned trajectory in order to
find the bilayer headgroup position and the bilayer thickness.
g_density works fine with the original trajectory but there seems to
be a bug when running
Thanks again Justin
-Original Message-
From: Justin A. Lemkul
Reply-to: "jalem...@vt.edu" , Discussion list for
GROMACS users
To: Gromacs Users' List
Subject: Re: [gmx-users] g_density CHARMM
Date: Tue, 11 Jan 2011 22:08:22 +0100
Ramon Guixà wrote:
> Justin,
A. Lemkul <mailto:%22justin%20a.%20lemkul%22%20%3cjalem...@vt.edu%3e>>
*Reply-to*: "jalem...@vt.edu" , Discussion list for
GROMACS users
*To*: Discussion list for GROMACS users <mailto:discussion%20list%20for%20gromacs%20users%20%3cgmx-us...@gromacs.org%3e>>
*Subj
: Justin A. Lemkul
Reply-to: "jalem...@vt.edu" , Discussion list for
GROMACS users
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] g_density CHARMM
Date: Tue, 11 Jan 2011 19:45:58 +0100
Ramon Guixà wrote:
>
> Dear all,
>
> I am just a newbie to Gromacs
Ramon Guixà wrote:
Dear all,
I am just a newbie to Gromacs so sorry for being naive with my questions...
I would like to yield electron density profiles out of different
trajectories of membranes simulated with NAMD and last CHARMM forcefield
(all_36_lipid_cholesterol). I first tried to us
Dear all,
I am just a newbie to Gromacs so sorry for being naive with my
questions...
I would like to yield electron density profiles out of different
trajectories of membranes simulated with NAMD and last CHARMM forcefield
(all_36_lipid_cholesterol). I first tried to use pdb2gmx in order to
gen
on. grompp probably reported the density when you made the .tpr, however.
Mark
- Original Message -
From: vferra...@units.it
Date: Tuesday, October 12, 2010 23:14
Subject: Re: [gmx-users] g_density options
To: jalem...@vt.edu, Discussion list for GROMACS users
Thanks a lot, but...
om: vferra...@units.it
Date: Tuesday, October 12, 2010 23:14
Subject: Re: [gmx-users] g_density options
To: jalem...@vt.edu, Discussion list for GROMACS users
> Thanks a lot, but... How can I exctract density information by
> using g_energy?
>
> Valerio
>
>
>
vferra...@units.it wrote:
Thanks a lot, but... How can I exctract density information by using
g_energy?
Have you tried it? You're given a list from which to choose. Type the number
of the property you want (i.e., Density), then either a blank line or the number
zero to terminate intera
Thanks a lot, but... How can I exctract density information by using g_energy?
Valerio
"Justin A. Lemkul" ha scritto:
Justin A. Lemkul wrote:
vferra...@units.it wrote:
I'm a GROMACS user and I want to authomatize solvent parametrization in
GROMOS force-field. The parametrization of a s
Justin A. Lemkul wrote:
vferra...@units.it wrote:
I'm a GROMACS user and I want to authomatize solvent parametrization in
GROMOS force-field. The parametrization of a solvent converg also on
the density. The problem is that g_density always ask on which element
of the system compute the dens
vferra...@units.it wrote:
I'm a GROMACS user and I want to authomatize solvent parametrization in
GROMOS force-field. The parametrization of a solvent converg also on
the density. The problem is that g_density always ask on which element
of the system compute the density and it is waiting for a
I'm a GROMACS user and I want to authomatize solvent parametrization in
GROMOS force-field. The parametrization of a solvent converg also on
the density. The problem is that g_density always ask on which element
of the system compute the density and it is waiting for a replay that
I can't authomat
Dear all,
I have a surface in xy plane. I want to use g_density to calcuate the density
profile of solvent along z axis. As my surface groups is not homogeneuously
distributed on the surface, some parts are hydrophilic and some parts are
hydrophobic. therefore I need to divide the surface into
minnale wrote:
Thanks Justin for your response just glance below
>> Hi all,
>>I have small doubt on g_density, The bilayer thickness can be
estimated by calculating density profile here I have calculated density
for different groups in lipid system by g_density command.
>>
>> The
Thanks Justin for your response just glance below
>> Hi all,
>> I have small doubt on g_density, The bilayer thickness can be estimated
>> by calculating density profile here I have calculated density for different
>> groups in lipid system by g_density command.
>>
>> The POPC density pro
minnale wrote:
Hi all,
I have small doubt on g_density, The bilayer thickness can be
estimated by calculating density profile here I have calculated density
for different groups in lipid system by g_density command.
The POPC density profile x-axis(z-nm) vs y-axis(density), it looks "
Hi all,
I have small doubt on g_density, The bilayer thickness can be estimated by
calculating density profile here I have calculated density for different groups
in lipid system by g_density command.
The POPC density profile x-axis(z-nm) vs y-axis(density), it looks "M" shape
what
Here are the answers to the questions:
Did see the trajectory. Looks fine
Did start from different initial time frames, and thicker slabs, problem
does not go away
Yes, the simulation has run for ~ 80 ns. It is equilibrated
Which log file ? What I reported was from the log file
On Tue, Jun 10
Have you seen the trajectory? Did you try to start from different frames? Is
your system equilibrated?
check log file!
Peyman
On Tuesday 10 June 2008 13:35, himanshu khandelia wrote:
> Hi,
>
> I am trying to calculate the density in a bilayer simulation:
>
> echo 27 | g_density -f lipiddrg.xt
Hi,
I am trying to calculate the density in a bilayer simulation:
echo 27 | g_density -f lipiddrg.xtc -n all.ndx -s all.tpr -o head.xvg
-sl 200 -b 4
The system size is about 6.5 x 6.5 x 9.6
I get the following error, after g_density has read most of the trajectory:
*** glibc detected *** g
Dear all,
The am studying a water-mesogen interface and when I am computing the density
profile of the water the curve is really smooth. On the other hand the density
profile obtained for the mesogen is really oscilating.
Do you have any ideas that could explain this behavior?
Thank you for you
Atoms.
- Original Message
From: Antonia Vyrkou <[EMAIL PROTECTED]>
To: gmx-users@gromacs.org
Sent: Tuesday, January 8, 2008 4:05:26 PM
Subject: [gmx-users] g_density
Dear all,
When using the g_density tool am I calculating the density of a group of
molecules in respect to the
Dear all,
When using the g_density tool am I calculating the density of a group of
molecules in respect to the atoms or to the center of mass of these molecules?
Thank you for your help
Antonia
__
Sent from Yahoo! Mail - a smarter
Hello,
I'd like to use g_density to obtain a density distribution plot. Now,
I'd like to place the center of that distribution on the zero of the
horizontal axis. How do I so using g_density? From reading the
manual, I see there's an option, "-center", which should do the trick.
But I've
Have a look at Makefile.am in the directory src/tools/ You can add
g(mx)_rdf_mod whereever you find g_rdf, following the logic of the
format. Then run automake (make sure it's the right version) and run
./configure from the gromacs directory. Finally, in src/tools/ issuing
make g_rdf_mod should th
Hi Chris,
Have a look at Makefile.am in the directory src/tools/ You can add
g(mx)_rdf_mod whereever you find g_rdf, following the logic of the
format. Then run automake (make sure it's the right version) and run
./configure from the gromacs directory. Finally, in src/tools/ issuing
make g_rdf_mo
Hi Chris,
Aren't you looking for a radial distribution function (g_rdf)? Maybe
you'll have to change the code a bit to get exactly what you want, but
I'd guess that g_rdf is closer to what you want. However, you do not
state what it is you want.., so it's merely a guess.
Best,
Of course you
Hi Chris,
Aren't you looking for a radial distribution function (g_rdf)? Maybe
you'll have to change the code a bit to get exactly what you want, but
I'd guess that g_rdf is closer to what you want. However, you do not
state what it is you want.., so it's merely a guess.
Best,
Tsjerk
On 11/10/
Does anybody have a modified g_density for calculation from the center
of mass of a micelle?
Thanks.
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