[gmx-users] Membrane protein simulation: maintain protein in the box centre

Anna Duncan anna.duncan at mrc-mbu.cam.ac.uk
Fri Jan 6 18:40:24 CET 2012


I've carried out simulation of a protein embedded in a membrane using  
the MARTINI coarse-grained force field. My simulation is 1 micro  
second long and towards the end of the simulation the protein drifts  
towards the 'edge' of the box.

In my analysis, I want to look at the minimum distance between each  
lipid 'atom' and the protein and, for each timepoint, record the  
residue or 'atom' in the protein that the lipid 'atom' is closest to.   
I can find the minimum distance using g_mindist but there is no option  
to record which residue or 'atom' in the protein the lipid 'atom' is  
closest to.

I've written my own scripts to look at minimum distances and record  
the closest-protein-residue information, but where the minimum  
distance is between the protein and the lipid atom's periodic image -  
when the protein is getting to 'the edge of the box' - these seem to  
be really slow running.

So the question is, is there a quick fix to get g_mindist to record  
the information I want it to (or even is there some other blindingly  
obvious function + special options that I've missed that will do the  
job)?  The other solution would be to edit the trajectory so that the  
protein always stays in the centre of the box.  I have already altered  
the trajectory, using g_traj and -pbc nojump (to remove jumps in the z- 
direction) then -pbc mol (to remove drift of lipids in the xy-plane),  
but I haven't managed to find anything that will maintain the protein  
in the box centre throughout the simulation.

Does anyone have any ideas? Please let me know if, as is usually the  
case, I've left out an important bit of information.

Many thanks,


More information about the gromacs.org_gmx-users mailing list