[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
(205) 690-0808 |
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