On Mon, Jan 14, 2013, Kirill Nuzhdin wrote:
>
> 1. How to set density for periodic system? Just by changing the size of
> the box at the end of a coordinate file?
Generally, one runs constant pressure simulations (at least during
equilibration) so that the density is adjusted to be that the force field
wants for the given external pressure.
You can indeed adjust the density by hand by chaning the box dimensions, but
if you made the box smaller than the actual dimensions of the atoms inside it,
you would get terrible overlaps that would probably crash the simulation.
>
> 2. What force field is reasonable to use for the system with quantized
> nuclei? (I have an impression that it was mentioned somewhere in the
> manuals, but I cannot find it)
The only ff specifically designed for quantized nuclei is q-spcfw.
>
> 3. addles is failing with the following error:
> ---------------
> LES was applied to solvent, atom 34
> This is not allowed.
> ---------------
> Why is it not allowed?
This check is not applied if you are using LES to create pimd (path integral
MD) input. So it looks like your input to addles is missing the "pimd"
option(?).
...dac
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Received on Tue Jan 15 2013 - 05:30:05 PST
