On 6/17/12 7:56 AM, delara aghaie wrote:
Dear Gromacs users.
I have simulated a single chain protein in water for 5 ns. Now I want to
calculate spatial distribution function. To do this I use command g_spatial. I
have read manual for that. I need to have an index group containing the atoms
arou
Dear Gromacs users.
I have simulated a single chain protein in water for 5 ns. Now I want to
calculate spatial distribution function. To do this I use command g_spatial. I
have read manual for that. I need to have an index group containing the atoms
around which the SDF is wanted.
It is not cle
I am trying to calculate spatial distribution function
(SDF) for ionic liquid.I want to see the distribution of anion around cation. I
followed the steps given in gromacs manual.I created two groups each of single
cation and all anions in the index file and did two steps trj
Here's the totally wasteful way for you to get what you want:
1. for each molecule in type A: trjorder everything around that
molecule and output only the closest N atoms of type A and the closest
M atoms of type B. Ensure that the coordinate order is: your central
molecule of type A is fir
Thanks Chris. I presume g_sdf won't be helpful for my system.
> I think that you have a misconception about what g_spatial does. For a
> system with many type A and many type B, you need to average over all
> of one type as the central solute to compute an rdf, and perhaps that
> is what you wan
I think that you have a misconception about what g_spatial does. For a
system with many type A and many type B, you need to average over all
of one type as the central solute to compute an rdf, and perhaps that
is what you want for your sdf. g_spatial, however, does not do any
fitting. g_sd
Dear all,
I'm working with a binary solvent mixture containing 2000 molecules (1800
type-A + 200 type-B). Both the types of solvent molecules have similar
structure (they are both diatomic molecules) except the polarity.I'm
trying to calculate sdf of type-B solvent molecules. I followed the
Dear all...
I want to get spatial distribution function for ionic liquid. So, I used g_sdf
command as below
g_sdf -f mixture_mdpr.trr -n index.ndx -s mixture_mdpr.tpr -o sdf_plt.dat -r
sdf.gro -mode 1 -grid 3.8 3.8 3.8
I rename the output file from .dat file to .plt file and I used VMD to view
es
Monash University
A polar bear is a Cartesian bear that has undergone a polar transformation
-Original Message-
From: gmx-users-boun...@gromacs.org on behalf of naimah haron naimah
Sent: Thu 12/3/2009 9:03 PM
To: gromacs
Subject: [gmx-users] spatial distribution function (SDF)
Hai all
g_spatial -h
-or-
g_sdf -h
-- original message --
ai all...
Did anyone know how to do spatial distribution functions??? I have 125
ion pairs in my system. The problem is,
1)how I can I get the 3-D probability distributions of anion around
cation or cation around anion in my system? Co
Hai all...
Did anyone know how to do spatial distribution functions??? I have 125 ion
pairs in my system. The problem is,
1)how I can I get the 3-D probability distributions of anion around cation or
cation around anion in my system? Could anybody tell me the method?
2)When I read the GROMACS
I am not sure what is going on in this case. You could try:
which g_spatial
to see what is being picked up. You could also try to move the
g_spatial executable to its own directory and then execute g_spatial
from that path:
/new/path/to/executable/g_spatial -h
ls /new/path/to/executable/g
HI Chris
I followed the steps below and when i tried to run g_spatial it executed
g_cluster instead. Even when i do g_spatial -h it looks like its being
overwritten by g_cluster
1.I used make_ndx to create a group containing the atoms around which i want
the SDF
2. trjconv -s md.tpr -f tyrc_
I wrote g_spatial and it should produce a spatial distribution
function. However, it's rather complicated to use. Did you follow the
directions in g_spatial -h ? There are about 10 steps to use it. It is
so complicated on purpose in order to give the user full flexibility,
but this means th
Gadzikano Munyuki wrote:
I want to analyse the solvent around a peptide . I used g_sdf and the output
that i am getting (i.e the refmol.gro) does not have the whole peptide molecule
but just the residues that i use to define the coordinate system . I then tried
to use g_spatialbut its doing s
I want to analyse the solvent around a peptide . I used g_sdf and the output
that i am getting (i.e the refmol.gro) does not have the whole peptide molecule
but just the residues that i use to define the coordinate system . I then tried
to use g_spatialbut its doing something very different and
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