Hi,
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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