Hi all,
I was curious as to thoughts on what is a sufficient amount of frames to
use for mmpbsa with and without entropy calculations. I have read various
papers and forum posts, and it seems as though everyone has differing
opinions. I am currently testing a few different configurations myself. For
my system, I have a 300ns production run, as well as 10 independent 10ns
production runs (both after 50ns of equilibration). Which would yield more
accurate results? I have read shorter, independent runs offer better data
compared to a longer, single run.
Furthermore, with the cluster I am using, I am unfortunately limited to
just under a week of simulation time per job, which after some testing, I
can get a 20 frame subset entropy calculation done (out of a total of 5000
frames). I am not sure if this subset is enough for an accurate result.
For example, in my .in file, if I specify nmendframe=5000, and
nminterval=250, which parameter would affect computation time more? If I
increase the end frame, or the interval; i.e. nmendframe=10000,
nminterval=500 vs. nmendframe=5000, nminterval=50? In other words, is it
better to do nm calculations on a higher number of overall frames and a
lower subset of frames, or a shorter amount of overall frames and a higher
number of subset frames? I would assume the higher the number in the
subset, the longer the computation?
I very much consider myself a novice at molecular dynamics as a whole, so I
hope this makes sense, haha.
Thanks in advance for your input.
Best Regards,
Alen
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jun 27 2019 - 20:30:02 PDT
