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

[Tsjerk Wassenaar]

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.parton at 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
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist