On 7/9/13 6:10 AM, maggin wrote:
Hi,
I have a qustion how to use g_cluster to judge convergence of the simulation
of peptide ?
Clustering can give you some insight into how homogeneous your structural
ensemble is. That is one way to assess convergence.
-Justin
--
==
Thanks for the report Sabine.
It would be nice if the original reporters could take the extra 5 seconds
to copy-paste and report the command lines they used. There are way too
many things that they or GROMACS could be doing wrong for any of us to
spend time guessing what is going on. :-)
Mark
O
Hi,
by looking into the code I could figure out some things.
WARNING: rmsd minimum 0 is below lowest rmsd value 0.0247473
This warning comes from the -rmsmin option which is set to 0 by default and
which controls the structure output.
The problem with tpr/gro files is that g_cluster uses mass
Hi,
I don't know. I don't know how to trigger it, and nobody has said how they
triggered it :-)
Mark
On May 14, 2013 4:45 PM, "Preeti Choudhary" <
preetichoudhary18111...@gmail.com> wrote:
> should we worry about the warning ???
>
>
> On Tue, May 14, 2013 at 7:19 PM, Mark Abraham >wrote:
>
> >
should we worry about the warning ???
On Tue, May 14, 2013 at 7:19 PM, Mark Abraham wrote:
> We'd need a lot more info to start to understand why .tpr vs .gro
> does/should affect the result (or not)!
>
> Mark
> On May 14, 2013 2:32 PM, "Sabine Reisser" wrote:
>
> > Hi,
> >
> > I'm having the s
We'd need a lot more info to start to understand why .tpr vs .gro
does/should affect the result (or not)!
Mark
On May 14, 2013 2:32 PM, "Sabine Reisser" wrote:
> Hi,
>
> I'm having the same warning, would also be interested in what it means.
>
> Additionally, I get different results if I use a t
Hi,
I'm having the same warning, would also be interested in what it means.
Additionally, I get different results if I use a tpr instead of a gro
file in the -s option, using the same trajectory with -f. The results
are completely different, for the gro file I get 42 while for the tpr
file I
On 3/27/13 5:40 AM, Zalikha Ibrahim wrote:
Good day to all GMX users,
I have two trajectories, 0-10ns and 10-20ns. I merged both .trr file using
trjcat with option -overwrite.
trjcat -f npt.trr npt2.trr -o npt_cat.trr -overwrite
Converted into .xtc and then I tried using the g_cluster tool
Hi Albert,
pdb is mentioned valid input for both -f (trajectory) and -s
(reference). So you can use the file you have for both:
g_cluster -s disco.pdb -f disco.pdb [...]
Cheers,
Tsjerk
On Tue, Apr 3, 2012 at 8:23 AM, Albert wrote:
> Dear:
>
> I've generated a disoc.pdb file by concoord and
Hi santhu,
maybe the differecence you observed depend by the xpm format.
In the xpm each cell is represented by one character that, in turn, is
represented as a color by xpm2ps.
Therefore the character count cannot be infinite so each character can
represent a range of RMSD cell.
In my opinion
On 21/07/2011 11:38 PM, Anna Marabotti wrote:
Hi folks
here I am with another kind of error, this time analysing my
trajectory of the rhombic dodecahedron dimeric system with g_cluster.
I used the following command:
g_cluster -f prot_boxdodfull_mol.xtc s prot_boxdodfull_molren.tpr -o
prot_boxd
Fixed!
Thank you!
On Jul 8, 2011, at 3:23 PM, Justin A. Lemkul wrote:
>
>
> Eric Fiedler wrote:
>> Hi,
>> I'm running Gromacs 4.5.1. Our group uses lammps for our simulations, but I'm
>> trying to use the g_cluster tool. I used VMD to convert trajectory files to
>> .trr and .pdb format, then a
Eric Fiedler wrote:
Hi,
I'm running Gromacs 4.5.1. Our group uses lammps for our simulations, but I'm
trying to use the g_cluster tool. I used VMD to convert trajectory files to
.trr and .pdb format, then attempt to run g_cluster using:
g_cluster -f traj.pdb -s trajstart.trr -g cluster.log -c
On 05/11/10 10:57, Fabio Affinito wrote:
On 10/31/2010 08:20 PM, Valeria Losasso wrote:
Dear all,
for my cluster analysis I am using the g_cluster tool with the gromos method.
The problem is that I have to compare the results for system of different
lengths, and of course the result of the clus
Hi all,
the problem is the type of the variable nrms. It is stored in as an int.
This means that whenever nframe*(nframe-1)/2 is greater than the maximum
positive value representable by a signed int there is an overflow and
nrms restarts from a negative value.
A workaround could be to declare n
On 26/03/11, Craig Kitchen wrote:
> Dear All,
>
> When running g_cluster on a file generated with g_mdmat I receive a
> segmentation fault. I have tried different versions of Gromacs (4.0.5 and
> 4.5.3) on different workstations with both large and small matrices - all
> without success.
>
Hi,
I am also trying to do clustering analysis, but g_cluster version 4.5.1
seems to have a bug. it does not crash but show strange std output like
# RMSD calculations left: -897758633
and the stopps after some time.
Which version do you guys use?
Best,
Xiaohu
On 11/05/2010 06:57 AM, Fab
On 10/31/2010 08:20 PM, Valeria Losasso wrote:
> Dear all,
> for my cluster analysis I am using the g_cluster tool with the gromos method.
> The problem is that I have to compare the results for system of different
> lengths, and of course the result of the cluster analysis changes according
> to
Shalom Andreas,
I suggest you would look into the RMSD distribution inside your clusters
(file namermsd-dist.xvg). In this file you will see one or more peak.
The cut off you use should be larger then this peak but smaller then the
second peak.
I know this is a bit simplicity, but for more
I'm not sure this is necessarily the case. Have you tried other methods
(gromos for example)? What are you getting when using other methods?
Regards,
-Shay
On Fri, Sep 17, 2010 at 6:14 PM, Kukol, Andreas wrote:
> Hi,
>
> I am using g_cluster to analyse a trajectory (protein backbone):
>
> g_clus
Hi,
The nearest neighbours are defined according to RMSD between the
structures. If M=10, a new conformation x is added to a given cluster
when a conformation y in the cluster exists such that:
(1) x and y are neighbours, i.e., x has y among the 10 conformations
with minimal RMSD to x and vice ver
Hi,
The distribution is calculated as follows:
101 bins are formed between zero and maximum rmsd in equal separation
(by calculating the largest value by 100 to create the separation). Each
rmsd value is put into the right bin and the counter for that bin is
increased by 1. The total number of cou
On 2010-03-02 00.13, ROHIT MALSHE wrote:
Hi All,
Greetings !
I have a question about g_cluster.
I have a configuration of Lennard Jones particles. For each particle I
calculate an individual bond orientational order parameter Q4. Based on
this order parameter I want to calculate the clusters i
edmund lee wrote:
Dear all,
When I am reading about the manual , I found that the g_cluster can
cluster structure with different type of methods, example, gromos,
monte-carlos and others.
Then I also found that g_clustsize computes the size distribution
function of the molecules or atoms. (co
sarbani chattopadhyay wrote:
Hi,
I have a query regarding "g_cluster" output.
I gave the command
g_cluster -f ../const_temp_20ns_0.pdb -s ../../md_0.tpr -sz -tr -cl -wcl
25 -cutoff 0.2
It is written in the "clusters.log" file that the middle structures of
each cluster is written in the
"clus
Hi,
Try -nofit
2 okt 2007 kl. 09.28 skrev andrea carotti:
Hi all,
I'm using this tool to cluter 2200 structures in this way:
fitting on the backbone, rmsd calculated on key residues (10) of the
Binding site.
Now I created the correct group in the index file and using the
g_cluster giving the t
Nikos Sgourakis wrote:
Hello,
I am trying to use g_cluster. However, the result I am obtaining when
using a pre-calculated RMSD matrix with the -dm option is quite
different than the one I get when the RMSD matrix is calculated by
g_cluster from a trjectory of structures. Is this a matter
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