On 03/22/2013 03:45 PM, Mark Abraham wrote:
As you can see in your plot, no replicas from 400K got down to 300K in the
1.5ns you simulated. So you've so far derived no benefit from REMD (unless
you want sampling at lots of temperatures). Perhaps a simulation a hundred
times longer might get a few such events? You might as well have run a
simulation at 400K to see what it did... What do you hope REMD will help
you observe?
Mark
HI Mark
thanks a lot for such kind advices and comments.
There is a ligand in my protein binding site and I hope REMD can
enable me how the ligand escape binding pocket coupled with some big
loop movement.
thank you very much.
best
Albert
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