Closed blakemertz closed 4 months ago
Hi Blake,
I believe Tinker9 (the GPU code) does not implement the active/inactive mechanism. If all you want to do is minimize an isolated protein molecule, then the CPU Tinker8 should be sufficient- unless you want to do lots of such minimizations.
The GPU code is missing lots of options that are in the CPU code. The whole goal of the GPU code is to be as fast as possible for standard all-atom MD simulations. And having lots and lots of options tends to slow things down.
@jayponder thanks for the quick response -- really appreciated. I didn't compile the documentation for T9 when I compiled this -- should have done that, as it would have been clear that the active/inactive functionality was missing. I re-ran this system using the restrain-position variable instead, calling a group of atoms that I had defined earlier in my key file -- this is essentially what I was looking to do, and it will give me more flexibility in defining the strength of the positional restraints I impose on my selected atoms.
I set a series of CA atoms in my protein to be inactive using the inactive parameter in my key file, but when I go to minimize the system, I get the following error:
My inactive line in my key file is as follows:
Is there something incorrect with my syntax? Also, is the 'inactive' keyword more appropriate or should I be using the 'restrain-position' keyword in my key file? I can define a group of atoms and then restrain them, but my reading of Jay's advice over in the T8 git issues https://github.com/TinkerTools/tinker/issues/73 is that I should be using the inactive keyword.