[gmx-users] gromacs.org_gmx-users Digest, Vol 154, Issue 114

Dayhoff, Guy gdayhoff at health.usf.edu
Thu Mar 30 16:38:10 CEST 2017

> Your approach to "fix" the Drude coordinates is inappropriate.  You're negating 
> (1) the purpose of equilibration by resetting the coordinates and (2) the 
> polarizable model entirely.

 Got it.

> The coordinate file provided on our website is already equilibrated and runs 
> indefinitely for me.  I don't know why your system is failing.  You are using 
> the latest checkout of the Drude branch, and you are running using only OpenMP, 
> not domain decomposition?

I’m not confident with respect to the last line here. I re-ran this using -ntmpi 1 -ntomp 32
and it runs just fine now. I suspect setting -ntmpi to 1 disables domain decomposition and
I was not doing this before. Working now. Thank you. 

-My Best
   Guy Dayhoff

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