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