[gmx-users] pbc atom

Gavin Melaugh gmelaugh01 at qub.ac.uk
Thu Aug 26 18:12:16 CEST 2010

O.K Chris

Thanks for all your help. I am actually considering removing the
thermostat all together seeing as my system is quite small.
I have also started using gen_vel = yes (no matter how much I think my
system is in equilibrium). One quick question (perhaps its silly). When
you say the initial forces become the initial velocities; I thought the
initial velocities were taken from the velocities in the initial
configuration (taking into account that I do have velocities in the
initial configurations from previous simulations).



chris.neale at utoronto.ca wrote:
> 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.
> Chris.
> -- 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
> Gavin

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