Dear Gromacs users
I have one big problem with g_clustsize!
I see 9 micelles in my system after running. When I use g_clustsize for number
of clusters and average cluster size, they don't emphasize each other, and I
see 9 micelles from 36 ps to 120 ps in my box, but results of
On 9/27/12 2:47 PM, mohammad agha wrote:
Dear Gromacs users
I have one big problem with g_clustsize!
I see 9 micelles in my system after running. When I use g_clustsize for number
of clusters and average cluster size, they don't emphasize each other, and I
see 9 micelles from 36 ps to
Dear Gromacs Users,
I don't know what is the quantity of -cut in g_clustsize for different systems,
exactly!
May I ask you to help me, Please?
Best Regards
Sara
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On 7/24/12 2:34 AM, mohammad agha wrote:
Dear Gromacs Users,
I don't know what is the quantity of -cut in g_clustsize for different systems,
exactly!
It is the cutoff value that determines if two molecules are in the same cluster.
If atoms in different molecules have a distance less
Dear Gromacs Users,
I have several questions about g_clustsize, Please help me.
I have several micelles in my system and I want to calculate: the number of
monomers in micelles and cluster number and monomer number during the time of
simulation, I used from this command as is follows:
Dear Gromacs Users,
I have several questions about g_clustsize, Please help me.
I have several micelles in my system and I want to calculate: the number of
monomers in micelles and cluster number and monomer number during the time of
simulation, I used from this command as is follows:
On 7/19/12 8:06 AM, mohammad agha wrote:
Dear Gromacs Users,
I have several questions about g_clustsize, Please help me.
I have several micelles in my system and I want to calculate: the number of
monomers in micelles and cluster number and monomer number during the time of
simulation,
Dear Justin,
Thank you very much from your response.
according you said I should set -cut with less than 0.7, but this doesn't
answer me!
for 0.6:
0.00e+00 115
6.00e+01 107
1.20e+02 114
1.80e+02 105
2.40e+02 100
3.00e+02
On 7/19/12 9:42 AM, mohammad agha wrote:
Dear Justin,
Thank you very much from your response.
according you said I should set -cut with less than 0.7, but this doesn't
answer me!
I didn't say that, but your results are completely consistent with what I said
about how g_clustsize is
Dear Justin,
Thank you very much from your help.
I think that I should work more on this command and will ask you next.
I don't know why does it bother me for it's .xvg and -tu !!!
Thank you very much again.
Best Regards
Sara
On 7/19/12 9:42 AM, mohammad agha wrote:
Dear Justin,
Thank
Dear Prof.
I have some problems about g_clustsize program and I didn't find my answer in
mailing list. Please help me.
I don't know what is the base of selection for -cut option?
In my system after doing g_clustsize, when I see nclust.xvg file, it looks like
all the atoms in the system were
On 2011-11-26 18:55, mohammad agha wrote:
Dear Prof.
I have some problems about g_clustsize program and I didn't find my
answer in mailing list. Please help me.
I don't know what is the base of selection for -cut option?
In my system after doing g_clustsize, when I see nclust.xvg file, it
looks
-users] g_clustsize
On 2011-11-26 18:55, mohammad agha wrote:
Dear Prof.
I have some problems about g_clustsize program and I didn't find my
answer in mailing list. Please help me.
I don't know what is the base of selection for -cut option?
In my system after doing g_clustsize, when I see
According to the description of the g_clustsize utility, it should
create the file temp.xvg containing the temperature of the largest
cluster versus time. While other files from g_clustsize are created
correctly, the temp.xvg is always empty. What is printed follows:
On 3/10/2011 1:55 PM, Dr. Vitaly V. Chaban wrote:
According to the description of the g_clustsize utility, it should
create the file temp.xvg containing the temperature of the largest
cluster versus time. While other files from g_clustsize are created
correctly, the temp.xvg is always empty.
Hi,
I am trying to use g_clustsize to follow aggregation of peptides. I am
currently using the following line:
g_clustsize -f my.trr -s ../my.tpr -nc nclusters.xvg -mol
Problem is, it actually counts monomers as clusters. I have a system
with 125 separate molecules, and the number of
On 2011-03-27 16.42, devicerandom wrote:
Hi,
I am trying to use g_clustsize to follow aggregation of peptides. I am
currently using the following line:
g_clustsize -f my.trr -s ../my.tpr -nc nclusters.xvg -mol
Problem is, it actually counts monomers as clusters. I have a system
with 125
On 27/03/11 16:29, David van der Spoel wrote:
On 2011-03-27 16.42, devicerandom wrote:
Hi,
I am trying to use g_clustsize to follow aggregation of peptides. I am
currently using the following line:
g_clustsize -f my.trr -s ../my.tpr -nc nclusters.xvg -mol
Problem is, it actually counts
On 2011-03-27 21.27, devicerandom wrote:
On 27/03/11 16:29, David van der Spoel wrote:
On 2011-03-27 16.42, devicerandom wrote:
Hi,
I am trying to use g_clustsize to follow aggregation of peptides. I am
currently using the following line:
g_clustsize -f my.trr -s ../my.tpr -nc nclusters.xvg
On 27/03/11 20:55, David van der Spoel wrote:
On 2011-03-27 21.27, devicerandom wrote:
On 27/03/11 16:29, David van der Spoel wrote:
On 2011-03-27 16.42, devicerandom wrote:
Hi,
I am trying to use g_clustsize to follow aggregation of peptides. I am
currently using the following line:
Hello everybody,
I'm using g_clustsize to analyze clusters formed in my solution.
However I noticed that not would get consistent results using the
complete trajectory (containing both solvent and solute). To see
the aggregation, using g_clustsize, I had to convert my trajectory
to a file
On 2010-05-22 00.28, toma0...@umn.edu wrote:
Hello,
Thanks for the response. g_clustsize outputs two xpm files of the
weighted and non-weighted cluster size vs time. Is there another way for
me to get number of clusters vs cluster size?
Not without programming, but since the information is
Hello,
Thanks for the response. g_clustsize outputs two xpm files of the
weighted and non-weighted cluster size vs time. Is there another way for me
to get number of clusters vs cluster size?
Thanks,
Mike
On May 20 2010, David van der Spoel wrote:
On 2010-05-20 04.55,
Hello,
I have a system of dimers which spontaneously assemble into clusters.
I would like to get a plot of the number of clusters of size s vs s. In
looking at g_clustsize I am able to obtain the average number of clusters
vs time, the average cluster size vs time and a histogram of the
On 2010-05-20 04.55, toma0...@umn.edu wrote:
Hello,
I have a system of dimers which spontaneously assemble into clusters. I
would like to get a plot of the number of clusters of size s vs s. In
looking at g_clustsize I am able to obtain the average number of
clusters vs time, the average cluster
It would be very advantageous for me to have a g_clustsize that
could implement the Jarvis-Patrick method instead of single linkage.
Would this be very difficult to achieve? Or would it be easy enough to
use source code from g_cluster and do a sort of transplant? Thank
you for you help
David
Jacob Spooner wrote:
It would be very advantageous for me to have a g_clustsize that
could implement the Jarvis-Patrick method instead of single linkage.
Would this be very difficult to achieve? Or would it be easy enough to
use source code from g_cluster and do a sort of transplant? Thank
you
I am planning on using g_clustsize to do some condensation analysis. I looked
at g_cluster and see that it has a number of method options including single
linkage and jarvis patrick. Is it true that g_clustsize has only the single
linkage option? I took a look at the source code but this type
Jacob Spooner wrote:
I am planning on using g_clustsize to do some condensation analysis. I looked
at g_cluster and see that it has a number of method options including single
linkage and jarvis patrick. Is it true that g_clustsize has only the single
linkage option? I took a look at the
Hi GMX Colleagues,
I need a little clarification.
I try to calculate a distribution of clusters of ions in a system with
several cations and anions and a few solvent molecules. So I just need
a number of cluster consisting of ions and the size of the each (how many
ions the cluster includes).
Hi GMX Colleagues,
I need a little clarification.
I try to calculate a distribution of clusters of ions in a system with
several cations and anions and a few solvent molecules. So I just need
a number of cluster consisting of ions and the size of the each (how many
ions the cluster includes).
Hi,
Use -n without -mol. Clustering will be atom based.
Good luck,
Ran.
Vitaly Chaban wrote:
Hi GMX Colleagues,
I need a little clarification.
I try to calculate a distribution of clusters of ions in a system with
several cations and anions and a few solvent molecules. So I just need
a
Hi Ran,
I will try your advice. And for what purpose should '-mol' be used?
Vitaly
RF Hi,
RF Use -n without -mol. Clustering will be atom based.
RF Good luck,
RF Ran.
RF Vitaly Chaban wrote:
Hi GMX Colleagues,
I need a little clarification.
I try to calculate a distribution of clusters
Hi Ran,
Then for what purpose should '-mol' be used?
In my case it's more convenient to have molecule-based clustering rather than
atom-based (in histo-clust.xvg, nclust.xvg, etc). Looking only at the
number of atoms in the cluster it is sometimes very difficult to
determine how many molecules
Vitaly Chaban wrote:
Hi Ran,
I will try your advice. And for what purpose should '-mol' be used?
To cluster molecules.
In this case, you topology is read from the .tpr file and all of the
molecules there are taken into account for clustering.
Vitaly
RF Hi,
RF Use -n without -mol.
RF In this case, you topology is read from the .tpr file and all of the molecules there are taken into account for clustering.
I think you are right but the following text from the g_clustsize help message has confused me:
"
When the -mol option is given clusters will be made out of
Vitaly Chaban wrote:
RF In this case, you topology is read from the .tpr file and all of the
molecules there are taken into account for clustering.
I think you are right but the following text from the g_clustsize help
message has confused me:
When the -mol option is given clusters will
DvdS Actually the text is incorrect (even the English is weird). If you use
DvdS the -mol flag the program will tell you that the index file is ignored.
DvdS If I recall correctly this wasn't always the case, and you could select
DvdS a subset of the molecules for this analysis. No clue why that
DvdS But is your index a molecular index now? I think it should be in those
DvdS versions.
I tried both cases. The result is the same as in the present version.
And the following comment is also present:
Using molecules rather than atoms. Not reading index file index.ndx
As for the error, it has
Dear GROMACS users and developers,
I am writing to ask for some help with using g_clustsize.
I have used g_clustsize with the following command line:
g_clustsize_d -f traj_no_water.xtc -s conf_no_water.tpr -mol -cut 0.3 -dt
1000
'traj_no_water.xtc' contains the trajectory of an ensemble
Alessandro Magliano wrote:
Dear GROMACS users and developers,
I am writing to ask for some help with using g_clustsize.
I have used g_clustsize with the following command line:
g_clustsize_d -f traj_no_water.xtc -s conf_no_water.tpr -mol -cut 0.3
-dt 1000
'traj_no_water.xtc' contains the
Dear GROMACS users and developers,
I have this error when using g_clustsize. Can anyone help me explain this?
Reading frame 0 time 14000.001 Reading file m24_16ns.tpr, VERSION 3.3.2
(single precision)
Reading file m24_16ns.tpr, VERSION 3.3.2 (single precision)
Group 0 (System) has
Dear GROMACS users and developers,
I have this error when using g_clustsize. Can anyone help me explain this?
Reading frame 0 time 14000.001 Reading file m24_16ns.tpr, VERSION 3.3.2
(single precision)
Reading file m24_16ns.tpr, VERSION 3.3.2 (single precision)
Group 0 (System) has
Alif M Latif wrote:
Dear GROMACS users and developers,
I have this error when using g_clustsize. Can anyone help me explain this?
Reading frame 0 time 14000.001 Reading file m24_16ns.tpr,
VERSION 3.3.2 (single precision)
Reading file m24_16ns.tpr, VERSION 3.3.2 (single precision)
Wang Zhun wrote:
Hi,
I'm working on peptide folding with GMX3.2.1 now. When I carried out
g_clustsize, it says:
Group 1 ( Protein) has 211 elements
Group 2 ( Protein-H) has 167 elements
Group 3 ( C-alpha) has22 elements
Group 4 (Backbone) has66
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