[gmx-users] pbc atom

chris.neale at utoronto.ca chris.neale at utoronto.ca
Thu Aug 26 16:00:20 CEST 2010

Gavin, I recall mentioning gen_vel=no with temperature coupling as a  
possible problem a while ago (the problem is that the initial forces  
become initial velocities and then those get scaled up and what you  
have are velocities and not temperatures -- read about the flying ice  
cube problem). Do you have any idea why it would only cause you  
problems at a distance of greater than 2 nm?

Also, Justin seemed to intuit this was a thermostat. I suspect that if  
you switch to the sd integrator things will all be ok. I don't really  
do anything in vacuum so it was harder to pick this up.

If you're tied to your md/NH settings, then you probably need to  
reduce the timestep -- but you will probaby run into problem  
eventually here too so I don't advise it.


-- original message --

Dear Chris and Justin

I ran a simulation for two water molecules (100 ns). It only took 5
minutes. Firstly I ran the simulation with ref distance 2.35 nm, genvel
=yes, and gen temp =600 (using Nose Hoover). This produced a histogram
with one main peak. I then took the final configuration from that
simulation and ran the simulation again for the exact same duration and
parameters etc, with the only exception that I set gen_vel = no. The
resulting histogram did indeed have two main peaks. I am now currently
running the simulation of my two cage molecules using berensden
thermostat to see if there is a difference.

Many Thanks


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