You ought to be able to use MERGE RECEnter to get the protein in the middle of the box in all frames.
I am not entirely familiar how recenter in detail works, but I only used it to eliminates translation of the entire system. But since the Protein is moving relative to the membrane this would have no effect on the protein moving around on the membrane. Please correct me if understood recentering wrong.
Another concern I do have regarding the recentering on the protein. If I should choose to recenter on the protein will this not influence the lipids I see passing/resting/following below the protein, will it? I am confused and I couldn't dissipate my doubt by reading the RECEnter notes in dynam.doc.
To save diskspace you could increase the write out frequency, say to 2500. This still gives you 200 frames/ns which is plenty for such a long simulation.
Well, I am not sure about this, since I once ran into trouble with a too low resolution (1ns) while calculating relaxation times. Comparing the simulation to the same setup with 100ps time resolution yielded different results. So far we didn't investigate any further but the difference might be related to the time resolution. So I'd rather throw in some more discs then throw away time by recalculating with a higher time resolution.
Deleting trajectories and storing reduced ones is quick and always possible ;-)
Thanks for your help and suggestions.
I appreciate it very much!