On Wed, Jan 16, 2013, Kirill Nuzhdin wrote:
> I skipped a lot of steps, so the questions I asked could be rather
> misleading, sorry for that. I'll try to explain what I did in more details.
>
> The main idea is to calculate simple radical in a water box.
OK... but radicals usually do "chemistry", and force fields descriptions do
not.
>
> 3. create LES, addles commands are:
But I don't understand *why* you want to use LES here.
The fact that you have chosen a "quantum" water model, and that you
mention "nuclear quantization" in your email certainly suggests that you were
led to LES by wanting to do a path-integral simulation; the easiest/best way
to do that is to quantize the entire system (see the "full_pimd" examples in
the test directory), and try to do that first. If you indeed want to quantize
only part of the system, make sure you study the "part_pimd" examples, *and*
make sure you use the "pimd" option in addles.]
>
> As for "exploding", maybe you are right about failure to image the
> resulting trajectory back to the primary unit cell. I'm not very
> familiar with how that could be done - where can I find the information
> about that?
Look at the ptraj (or cpptraj) chapters in the AmberTools Reference Manual.
...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jan 16 2013 - 14:00:02 PST
