Hi Daniel, 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, Tsjerk On Mon, Nov 30, 2009 at 12:24 PM, Daniel Parton <daniel.par...@bioch.ox.ac.uk> wrote: > 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 > > -- > gmx-users mailing list gmx-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
