Gromacs manual explains radial distribution function gAB (r, theta)
but g_rdf donot have options to directly do this.
Can anyone elaborate this.
--
Best regards
Neshatul Haque
PhD, Dpt of Biotechnology
university of hyderabad
--
gmx-users mailing listgmx-users@gromacs.org
On 6/24/13 9:05 AM, neshat haq wrote:
Gromacs manual explains radial distribution function gAB (r, theta)
but g_rdf donot have options to directly do this.
Can anyone elaborate this.
That section probably refers to a feature that was intended to be included but
was never developed. Such
Gromacs manual explains radial distribution function gAB (r, θ)
but g_rdf donot have options to directly do this.
Can anyone elaborate this.
--
Best regards
Neshatul Haque
PhD, Dpt of Biotechnology
university of hyderabad
--
gmx-users mailing listgmx-users@gromacs.org
Hi,
I have a system that is effectively two-dimensional. I have two parallel
plates, which are each parallel to the xy plane. Thus, I have what I think
one would call slab geometry.
Since my system is clearly not isotropic, it does not make sense to compute
radial distribution functions in the
On 4/22/12 5:39 PM, Andrew DeYoung wrote:
Hi,
I have a system that is effectively two-dimensional. I have two parallel
plates, which are each parallel to the xy plane. Thus, I have what I think
one would call slab geometry.
Since my system is clearly not isotropic, it does not make sense
Hello everyone,
Is there any way to do a g(r) plot between the COM of a single solute
particle, and the COMs of each solvent molecule around it? It seems to
only let your choice be the COM for the first pick. Is there any way to do
it for both choices?
Thanks.
--
Best regards,
Fabian F.
Fabian Casteblanco wrote:
Hello everyone,
Is there any way to do a g(r) plot between the COM of a single solute
particle, and the COMs of each solvent molecule around it? It seems to
only let your choice be the COM for the first pick. Is there any way to
do it for both choices?
I
is a hammer, every problem begins to resemble a nail.
From: Moeed [mailto:lecie...@googlemail.com]
Sent: Saturday, 17 September 2011 1:58 AM
To: Discussion list for GROMACS users
Cc: Dallas Warren; tsje...@gmail.com
Subject: Re: [gmx-users] radial distribution function
Thank you Dr Warren for your
-users] radial distribution function
** **
Hello again,
I tried comparing RDF plots generated by sampling from 4 to 5 ns run and a
longer run from 4 to 30 ns to see whether the small jumps on the plot are
due to insufficient sampling. Attached is the new plot showing that two RDF
curves
Hello again,
I tried comparing RDF plots generated by sampling from 4 to 5 ns run and a
longer run from 4 to 30 ns to see whether the small jumps on the plot are
due to insufficient sampling. Attached is the new plot showing that two RDF
curves are almost identical. I only wanted to let you know
Sent: Friday, 16 September 2011 12:55 AM
To: jalem...@vt.edu; Discussion list for GROMACS users
Subject: Re: [gmx-users] radial distribution function
Hello again,
I tried comparing RDF plots generated by sampling from 4 to 5 ns run and a
longer run from 4 to 30 ns to see whether the small jumps
begins to resemble a
nail.
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Moeed
Sent: Friday, 16 September 2011 12:55 AM
To: jalem...@vt.edu; Discussion list for GROMACS users
Subject: Re: [gmx-users] radial distribution function
Hello again,
I
Thank you for your input. I am going to run for another 15 ns to see if the
little jumps vanish.
Best,
On Fri, Sep 9, 2011 at 9:16 PM, Justin A. Lemkul jalem...@vt.edu wrote:
lina wrote:
On Sat, Sep 10, 2011 at 3:35 AM, Moeed lecie...@googlemail.com mailto:
lecielll@googlemail.**com
On Sat, Sep 10, 2011 at 10:00 PM, Moeed lecie...@googlemail.com wrote:
Thank you for your input. I am going to run for another 15 ns to see if the
little jumps vanish.
Best,
g_rdf -bin
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gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Dear users,
I have created radial distribution function plot for Carbon atoms in a
system containing polymer chains. I see some little jumps between first and
second peak.
I need your help to comment on how this behavior can be justified (or if the
plot is wrong).
g_rdf -f *.trr -s *.tpr -o
Moeed wrote:
Dear users,
I have created radial distribution function plot for Carbon atoms in a
system containing polymer chains. I see some little jumps between first
and second peak.
I need your help to comment on how this behavior can be justified (or if
the plot is wrong).
g_rdf -f
Thank you Justin for your reply. Simulation is 5 ns long ( before this a 500
ps NVT was done as equilibration) and total energy has been equilibrated
after around 3 ns.
-b is set to 4000 that is the last 1 ns has been used for rdf.
Best,
moeed
On Fri, Sep 9, 2011 at 3:37 PM, Justin A. Lemkul
Moeed wrote:
Thank you Justin for your reply. Simulation is 5 ns long ( before this a
500 ps NVT was done as equilibration) and total energy has been
equilibrated after around 3 ns.
-b is set to 4000 that is the last 1 ns has been used for rdf.
For all but the simplest systems this
On Fri, Sep 9, 2011 at 4:18 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Moeed wrote:
Thank you Justin for your reply. Simulation is 5 ns long ( before this a
500 ps NVT was done as equilibration) and total energy has been equilibrated
after around 3 ns.
-b is set to 4000 that is the
Moeed wrote:
On Fri, Sep 9, 2011 at 4:18 PM, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu wrote:
Moeed wrote:
Thank you Justin for your reply. Simulation is 5 ns long (
before this a 500 ps NVT was done as equilibration) and total
energy has been
On Sat, Sep 10, 2011 at 3:35 AM, Moeed lecie...@googlemail.com wrote:
Dear users,
I have created radial distribution function plot for Carbon atoms in a
system containing polymer chains. I see some little jumps between first and
second peak.
I need your help to comment on how this behavior
lina wrote:
On Sat, Sep 10, 2011 at 3:35 AM, Moeed lecie...@googlemail.com
mailto:lecie...@googlemail.com wrote:
Dear users,
I have created radial distribution function plot for Carbon atoms in
a system containing polymer chains. I see some little jumps between
first and
Hello every1,
I have a question about interpretation of g_rdf.
I have generated a plot with g_rdf (with -com flag) of a nanoparticle in
water, and it shows an unstable graph (y-axis) the first picoseconds , and
then a smoothing of the curve towards the zero the more r-value on the
x-axis
Hi All,
I would like to compute the radial distribution
function g(r) between solvent molecules and a group of
atoms of the solute. To this end, I define two groups
in the index.ndx file: one for solvent and one for a
peptide group. The index file looks like:
[ Pep ]
1
2
3
4
[ Sol]
10
11
12
-
From: Qiao Baofu
To: Discussion list for GROMACS users
Sent: Wednesday, November 22, 2006 1:39 PM
Subject: Re: [gmx-users] radial distribution function
To my knowledge, g_rdf calculate all the atoms of group A to all the atoms of
group B to get the gAB(r). g_rdf -com calculate
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