Hi everyone,
I have noticed that during a TAD (using IVM) at 303 K, the temperature
variations were around +/- 30 K. I am currently working on a di-ubiquitin
system with amber force field (no experimental constraints, backbone fixed),
>20000 steps, 50 ps. If I use only one monomer, the variations are almost the
same and if I switch this system to standard xplor forcefield, the variations
are more like +/- 10 K. I have few experience with MD, are those variations
reasonable or should I correct something ?
I am also trying to use implicit solvent with Generalized Born (hence
the amber forcefield). Though I was expecting a longer computing time, I have
something like a 100 folds increase. It seems a lot to me, from the GB test
files, I was expecting something like a 5 fold increase. Anyone with feedback
on that point ?
Thank you for your attention,
Olivier Serve
