[gmx-users] mdrun in vacuum diverging? -- possibly due to nopbc?

Mark Abraham Mark.Abraham at anu.edu.au
Sun Mar 5 05:41:26 CET 2006

Yousung Jung wrote:
> Dear more experienced users,
> My system is a water/methanol mixture with 100 and 300 molecules for 
> water and methanol, respectively. I equilibrated the system with pbc for 
> 500 ps at 300K in vacuum. Then, I ran the actual simulation at 235K in 
> vacuum WITHOUT pbc to simulate a droplet of the mixture. I see a few 
> water and methanol molecules escaping "the system" (or, the droplet) 
> during the simulation.
> The problem that I am struggling with for this system is, after about 
> 400 ps of the actual dynamics at 235K, temperature starts fluctuating 
> badly, getting worse until the simulation stops at around 600 ps. When I 
> visualize the trajectory, I see the system (a droplet in vacuum) 
> rotating and translating at around the same time as the temperature 
> begins fluctuating. I did use comm_mode = angular to eleminate rot. and 
> trans. modes.
> I reduced the time-step to 0.5 fs, but the problem still exists (the 
> system translating significantly in vacuum). Is it possible that this is 
> due to the fact that the center of mass is used for removing 
> translational and rotational motion and a few escaped molecules are 
> causing this problem? (If those ones that are escaping are causing the 
> problem, I guess I could use pbc with a "big" box.) Assuming this is the 
> case, I have two questions:

One approach is to have a shell of waters on the outside that have 
positition restraints. Now you have an effectively impermeable barrier. 
Your boundary effects will be a bit different, but perhaps a bit milder.


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