Hello Angelica,
I quickly comment on only two of your issues, see below.
On 04.05.2013 11:08, Angelica Parente wrote:
> I've tried looking at the trajectories (~34000 frames, 64ns) in VMD,
> but VMD crashes after loading in about ~7000 frames.
VMD loads trajectory data into RAM. Most likely, after reading about
7000 frames your RAM is full. The OS starts to swap, and VMD/the machine
becomes unresponsive. Solution: in the file opening window, VMD gives
you the option to only read every Nth frame from the trajectory (this is
called "step" or "interval"). Load every 7th frame, i.e. about 5000 in
total, and you can visualize the entire trajectory with decreased time
resolution.
> the MMPBSA results I get for those are very
> strange (PB total free energy difference is ~ +1000kcal/mol due to
> high non-polar free energy components,
That problem has just been discussed on the list, see this thread:
http://archive.ambermd.org/201304/0482.html
It's the result of an issue in PBSA code -- I think an official fix is
going to be released soon.
Cheers,
Jan-Philip
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Received on Sat May 04 2013 - 09:30:02 PDT
