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

Peter C. Lai pcl at uab.edu
Fri Jan 6 19:19:57 CET 2012

On 2012-01-06 05:40:24PM +0000, Anna Duncan wrote:
> 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.

g_mindist -o atm-pair.out will give you atom min distance pairs within
-d cutoff over the length of the trajectory.

> 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.

-center and pick the protein c-alpha as the centering group

Peter C. Lai			| University of Alabama-Birmingham
Programmer/Analyst		| KAUL 752A
Genetics, Div. of Research	| 705 South 20th Street
pcl at uab.edu			| Birmingham AL 35294-4461
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