[gmx-users] R: Re: g_cluster error in rhombic dodecahedric system (Mark Abraham)

[Anna Marabotti]

Thanks Mark for suggestion, I'll try to do a simpler clustering method. In
the meantime, I only would like to add a further info: I pre-processed my
trajectory following someone's (Justin, IIRC) suggestion in a previous
message, using trjconv -pbc mol -ur compact. So, in my trajectory the
molecules should be whole (at least, I see my protein as a whole). This
pre-processing was necessary because with trjconv -pbc whole I was not able
to have my homodimeric protein in the unit cell: the protein was split in
two monomers in two adjacent unit cells. Could be the presence of the two
identical monomers to "confuse" Gromacs that sees an RMSD minimum of 0?
Anna

-----Messaggio originale-----

Message: 2
Date: Fri, 22 Jul 2011 00:25:03 +1000
From: Mark Abraham <Mark.Abraham at anu.edu.au>
Subject: Re: [gmx-users] g_cluster error in rhombic dodecahedric
	system
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4E2836BF.3000800 at anu.edu.au>
Content-Type: text/plain; charset="iso-8859-1"

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_boxdodfull_clust.xpm -sz prot_boxdodfull_clustsize.xvg -tr 
> prot_boxdodfull_clusttrans.xpm -ntr prot_boxdodfull_clusttrans.xvg 
> -clid prot_boxdodfull_clustovertime.xvg -cl 
> prot_boxdodfull_clusters.pdb -av -cutoff 0.25 -method gromos -b 10000

I'd suggest starting with a small trajectory and a basic clustering 
method to help you eliminate possible sources of problems. If things are 
working, add complexity.

> (the command is inspired to that shown in Tsjerk's tutorial, with some 
> changes, and with the missing -g flag - I forgot to add it). For both 
> least square fit+RMSD calculation and output I used option 2 (Protein-H).
> The .tpr file is derived from the renumbered .gro file in which I can 
> see both subunits of my protein (as suggested sometimes ago by 
> Justin), created with the command: grompp -f full.mdp -c 
> prot_boxdodfull_molren.gro -o prot_boxdodfull_molren.tpr -p topol.top, 
> in which full.mdp is the file I used for the full MD.

I don't think you need a new .tpr, or a .tpr at all. Nothing about the 
clustering method requires knowledge of molecule or parameter 
definitions, so the original .tpr or the coordinate file that made it 
will do. Surely the clustering is based on RMS after fitting of the two 
structures under consideration, and now even the coordinates in the 
g_cluster -s file don't matter. Pre-processing the trajectory can matter 
- you probably want whole molecules in the simulation cell.

Mark

> With this command, I obtained the following output, that I'm copying 
> and pasting here (I cut some parts because of the length of the 
> message, but I think they are not necessary):
>
> Reading frame 0 time 10000.000
>
> Reading frame 1 time 10005.000
>
> Reading frame 2 time 10010.000
>
> Reading frame 3 time 10015.000
>
> Reading frame 4 time 10020.000
>
> Reading frame 5 time 10025.000
>
> Reading frame 6 time 10030.000
>
> ............................................
>
> Reading frame 3000 time 25000.000
>
> Reading frame 4000 time 30000.000
>
> Last frame 4000 time 30000.000
>
> Allocated 280347120 bytes for frames
>
> Read 4001 frames from trajectory prot_boxdodfull_mol.xtc
>
> Computing 4001x4001 RMS deviation matrix
>
> # RMSD calculations left: 7998000
>
> # RMSD calculations left: 7994001
>
> # RMSD calculations left: 7990003
>
> # RMSD calculations left: 7986006
>
>
............................................................................
...........
>
> The RMSD ranges from 0.0776069 to 0.282556 nm
> Average RMSD is 0.18743
> Number of structures for matrix 4001
> Energy of the matrix is 281.481 nm
> WARNING: rmsd minimum 0 is below lowest rmsd value 0.0776069
> Making list of neighbors within cutoff
>
> Finding clusters1
>
> Found 1 clusters
>
> Writing average structure for each cluster to prot_boxdodfull_clusters.pdb
> Counted 0 transitions in total, max 0 between two specific clusters
>
> -------------------------------------------------------
> Program g_cluster, VERSION 4.5.3
> Source code file: matio.c, line: 953
>
> Fatal error:
> hi (0.000000) <= lo (0.000000)
> For more information and tips for troubleshooting, please check the 
> GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> I tried to look at the documentation, but found only 1 similar 
> problem, using the g_rmsdist command, but there is not a solution to 
> the problem. I see the warning message claiming that the rmsd minimum 
> 0 is below lowest rmsd value, but I don't know how to manage it. Could 
> the .tpr file I used be the cause of the problem?
> Could anybody help me please?
> Thank you so much for your continue support
> Anna
> __________________________________________________________________
> Anna Marabotti, Ph.D.
> Laboratory of Bioinformatics and Computational Biology
> Institute of Food Science - CNR
> Via Roma, 64
> 83100 Avellino
> Phone: +39 0825 299651
> Fax: +39 0825 781585
> E-mail: amarabotti at isa.cnr.it <mailto:amarabotti at isa.cnr.it>
> Skype account: annam1972
> Web site: http://bioinformatica.isa.cnr.it/anna/anna.htm
> "When a man with a gun meets a man with a pen, the man with the gun is 
> a dead man"
> (Roberto Benigni, about Roberto Saviano)
>
>

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