[gmx-users] Problems with the SHAKE-algorithm -> is a problem of energy conservation
Mark.Abraham at anu.edu.au
Wed Mar 8 00:04:06 CET 2006
Björn Fischer wrote:
> David van der Spoel wrote:
>> At high temperature you need a shorter time step. Are you sure you
>> don't want to use T-coupling?
> Thanks for the advice,
> it didn't solve the problem, but it took me one step further to the
> solution. I should have been more specific about my system:
> Its an argon/nonane (2:1) system at 600 K. The normal timestep is 1.0
> fs, I also used 0.5 fs and 0.1 fs for testing purposes.
> Only the argon is coupled to the heatbath.
> The Shake-problem is only a symptom, the real problem is that the energy
> is not conserved (checked via a NVE-run).
> The total energy is conserved for a time (for example about 60000
> timesteps) , then jumps upward fourfold over about 1000 timesteps.
> After that the SHAKE-problems starts. Making the timestep smaller
> doesn't solve the problem.
> Do you have any suggestions, why the energy is not conserved (apart from
> a wrongly implemented force field) ?
You've only coupled a small minority of your atoms in the simulation to
the heat bath. I can't support my opinion, but that strikes me as asking
for trouble. I just think the transfer of heat between argon and nonane
won't be good (enough) to stabilize the system. I think you're right
about the SHAKE problem being a symptom, though.
More information about the gromacs.org_gmx-users