Dear amber users,
I am working with membrane proteins and planing to do a microsecond long
simulation. I have few queries for which I would like to get your expert
suggestions.
1. I have seen from literature that many membrane protein simulations are
carried out with Gromacs and NAMD engine. Since I am familiar with Amber, I
wish to stick with Amber for the simulation. How safe to go with Amber for
microsecond long membrane protein simulations?
2. All my previous simulations were of 100-200ns. I ran the simulations
with 5 ns window and saving the trajectories every 2 ps. Here, since the
simulations are going to be microsecond long, How good to stick with the
same protocol.?. I am very much aware of the large dataset going to be
generated during this long run.
Waiting for your valuable suggestions
Thanks in advance
Anu
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Apr 29 2015 - 06:30:03 PDT
