Hello
I am trying to look at hbond lifetimes in an aqueous electrolyte using Amber16. The simulation box contains 550 WAT and lots of ions. The simulation is 50ns long with 1ps timesteps at 333K.
Running the following works a treat:
trajin MD333.mdcrd
hbond water donormask :WAT acceptormask :WAT.O out hbond.dat avgout hbavg.dat
go
And I get hbond.dat (1MB) which as I understand states for every frame how many hbonds are present, as well as hbavg.dat (16MB) which lists every individual hbond and for how many frames in total it was present. Correct?
When I try to do a lifetime analysis with the following command
trajin MD333.mdcrd
hbond water donormask :WAT acceptormask :WAT.O out hbond.dat avgout hbavg.dat series uuseries hbseries.gnu nointramol
go
lifetime water[solutehb] out hbwater-lifetime.dat
go
I do get the hbwater-lifetime.dat file but it is enormous (after 10GB I stopped).
Did I do something wrong or is this normal for a system containing many WAT? If yes, what's the best way to handle such large files in order to extract relevant information? Basically I want to compare two electrolytes and see if there's differences in hbond dynamics.
Thank you in advance for any hints!
David
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Received on Wed May 15 2019 - 03:00:02 PDT
