On 19/07/17 19:18, antra saxena wrote:
Hello,
I have a question regarding g_clustsize.
I have a multi-peptide system and I want to determine the size of the
cluster.
As far as I understand, g_clustsize will cluster molecules (with -mol
option) within each frame of a trajectory within the
Hello,
I have a question regarding g_clustsize.
I have a multi-peptide system and I want to determine the size of the
cluster.
As far as I understand, g_clustsize will cluster molecules (with -mol
option) within each frame of a trajectory within the cutoff distance
specified.
With -nc option,
On 06/07/15 06:05, V.V.Chaban wrote:
The sum of these probabilities is never the same. It is confusing.
If no clusters exist (all particles are lone) then the sum of
probabilities equals the sum of all particles. If clusters exist, the
sum is different and it is unclear how it is derived.
If
g_clustsize creates file 'histo-clust.xvg'. What does y-axis in this file mean?
If this is a probability than of what?
@title Cluster size distribution
@xaxis label Cluster size
@yaxis label ()
@TYPE xy
0 0.000
128.385
2 7.135
3 1.552
4
On 05/07/15 14:09, V.V.Chaban wrote:
g_clustsize creates file 'histo-clust.xvg'. What does y-axis in this file mean?
If this is a probability than of what?
Probability of cluster size, what else?
@title Cluster size distribution
@xaxis label Cluster size
@yaxis label ()
@TYPE
The sum of these probabilities is never the same. It is confusing.
If no clusters exist (all particles are lone) then the sum of
probabilities equals the sum of all particles. If clusters exist, the
sum is different and it is unclear how it is derived.
If the output property is still a
Hi,
If the cluster size is constant, what is there to analyze?
Mark
On Mon, May 25, 2015 at 4:13 PM pratibha kapoor kapoorpratib...@gmail.com
wrote:
Thanks Mark for your reply.
I would like to extract chain ids of all the members of the maximum
populated cluster at each point of time. Thus,
I would like to enlist the chain ids (A,B,C...) , of all those which are in
cluster at each time frame.
Thanks in advance
On Mon, May 25, 2015 at 7:43 PM, pratibha kapoor kapoorpratib...@gmail.com
wrote:
Thanks Mark for your reply.
I would like to extract chain ids of all the members of the
Thanks Mark for your reply.
I would like to extract chain ids of all the members of the maximum
populated cluster at each point of time. Thus, I have created a script that
would run g_clustsize at each time frame which is giving me error:
Fatal error:
Lo: 0.00, Mid: 16.00, Hi: 16.00
Hi,
I don't understand how you can have a problem with one cluster, when the
size of that cluster is constant, but the identities of the members of the
cluster is not constant.
There may be a bug in gmx clustsize, which you might fix or hack around. If
not, I guess you have to find a way to have
Hi,
I have used g_clustsize to count the number of molecules (they differ by
chain id) in the maximum populated cluster. Is it also possible to label
these molecules? i.e. to print chain ids of these molecules with time in
separate file?
Thanks in advance
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Hi,
No, but you can probably use -mcn to get an index group of the atoms, and
work backwards from there. See gmx clustsize -h
Mark
On Tue, May 19, 2015 at 6:07 PM pratibha kapoor kapoorpratib...@gmail.com
wrote:
Hi,
I have used g_clustsize to count the number of molecules (they differ by
I can observe that GM1 molecules are separating from the DPPC molecules into
GM1 domains. Is it possible to calculate the number of GM1 molecules in these
GM1 domains? It worked with g_clustersize -cut 0.5 without the -mol option. I
use the Martini force field.
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Hi Raisa,
I guess you know how many atoms are in a molecules, so you can divide the
clustersize in atoms by it to get the number of molecules. Probably the
biggest problem is that the output is in XPM format? I have a script
(attached) to convert that to generic .dat format, which you can then
On 2014-06-12 15:33, Raisa Kociurzynski wrote:
Dear Prof. Van der Spoel,
I want to calculate the clustersize of GM1 clusters in a DPPC membrane. I used
g_clustersize but when I use the option -mol the index file is ignored and the
whole system is used for the calculation. Is there any way to
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