On 1/16/2013 4:35 PM, David A Case wrote:
> 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.
True. But I am looking at the time intervals when these radicals do not
do any chemistry.
>> 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.]
I used LES instead of full PIMD in order to reduce the system size. As
far as I understand, to get reasonable results, I need to use 24-32
beads for H atoms. If a system contains 200 water molecules, full PIMD
will result in 200*3*24=14400 particles, while LES - in
200*(2*24+1)=9800 particles.
I studied part_pimd examples and have not found any "pimd" option used
for addles command, sorry (even studied "grep -ir pimd
$AMBERHOME/test/PIMD/part_*" output).
So it looks like the easiest way is to try full PIMD.
>> 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.
OK, an image command will help to wrap molecules back to primary unit
cell after some modifications are done to the system, but how
coordinates are saved to a restart file - as coordinates for the images
within primary unit cell, or absolute coordinates of original molecules?
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Received on Wed Jan 16 2013 - 15:30:04 PST
