[CP2K-user] Thoughts on RDFs for NPT ensemble simulations?

[Travis]

Hi,

You need to use the logfile from your simulation to extract the box sizes 
at timesteps you dumped coordinates. You can then rerun your trajectory 
with CP2K (REFTRAJ ensemble) and convert it to DCD_ALIGNED_CELL format. 
This format stores positions and lattice parameters. You then load the XYZ 
file (for atom names) and DCD file into VMD. Now you can compute a RDF with 
variable box size. In the future, always dump coordinates from constant 
pressure simulations to DCD_ALIGNED_CELL. PDB format would work too.

-T


On Monday, August 26, 2019 at 8:18:32 AM UTC-3, Ant wrote:
>
> I'd like to add, for anyone else who is checking in here, that I would be 
> very interested to know what people think about simply using an average 
> volume for an NPT RDF--if it is too sloppy or if it makes sense, at least 
> until I figure out how to use distinct volumes at each time step.
>
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