[gmx-users] trjconv -pbc cluster with rhombic dodecahedron box
tsjerkw at gmail.com
Mon Nov 30 13:48:17 CET 2009
This doesn't exactly answer your question, but if your vesicle is
whole at the start, can't you better keep it that way using -pbc
nojump? If necessary, you can also recenter afterwards.
Hope it helps,
On Mon, Nov 30, 2009 at 12:24 PM, Daniel Parton
<daniel.parton at bioch.ox.ac.uk> wrote:
> 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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Tsjerk A. Wassenaar, Ph.D.
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