[gmx-users] trjconv -pbc cluster with rhombic dodecahedron box

Daniel Parton daniel.parton at bioch.ox.ac.uk
Mon Nov 30 12:24:58 CET 2009


I am running a coarse-grained simulation of a lipid vesicle (~70,000 
particles), using a rhombic dodecahedron box to limit the amount of 
solvent I require.  The vesicle (unsurprisingly) moves over the periodic 
boundaries during the simulation.  Various analyses I am conducting 
require the vesicle to be whole, so I have been trying to use trjconv 
with the -pbc cluster option, selecting the lipids as the group to be 
clustered.  I am only interested in the lipid behaviour, so I am using a 
trajectory with only the lipids included.  However, at certain frames, 
the program seems to enter an infinite loop, producing many lines of the 
following sort of information:

COM:   12.445     5.934    15.354  iter = 2359
COM:   12.675     6.135     3.094  iter = 2360
COM:   12.455     5.934    15.368  iter = 2361
COM:   12.686     6.131     3.116  iter = 2362
COM:   12.454     5.945    15.396  iter = 2363
COM:   12.720     6.168     3.176  iter = 2364
COM:   12.461     5.947    15.435  iter = 2365
COM:   12.731     6.174     3.221  iter = 2366
COM:   12.468     5.945    15.475  iter = 2367
COM:   12.723     6.172     3.247  iter = 2368

This is using gromacs version 3.2.1, as with any later version I have 
tried (3.3.3, 4.0.4, 4.0.5), trjconv -pbc clust  won't work at all, even 
with cubic simulation boxes.  I have successfully used version 3.2.1 
many times for this purpose when dealing with cubic simulation boxes.

I have tried many different ways to get this to work, such as converting 
to the compact representation before clustering.  Also, the frame where 
the program is the first one where a lipid has moved over a periodic 
boundary, when the system is viewed as the compact representation.  The 
same behaviour occurs when that frame is dumped out as a .gro file and 
the program is run on that file only.

Does anyone have any idea how to get this to work?  Any help would be 
much appreciated!  Please let me know if you need more information about 
my simulation set-up.

Daniel Parton

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