After weeks of trying various conditions, I found my problem. Here, from my position-restrained MDP file, are the two relevant lines:
; Temperature coupling is on tcoupl = V-rescale ; Weak coupling for initial equilibration [snip] ; Pressure coupling is on pcoupl = Berendsen ; Pressure coupling on in NPT, also weak coupling This is a change that I forgot to mention in my list of changes, but in fact I did post the full MDP file. I switched to using two DIFFERENT algorithms for temperature and pressure coupling when I performed the initial position-restrained equilibration. This frequently sets up an INSTABILITY which manifests itself anywhere from a few picoseconds to a full nanosecond into the standard equilibrium MD run. I am giving this number in real time, rather than in compute cycles, because I tried cutting my step time to 1.0 fs from my usual 2.0 fs -- and I still had a water molecule dislocate abruptly, at nearly the same physical location and simulated time point. I will share my full debugging process if anyone is interested. It took me several runs, all of them over 24 hours long, to figure this out. Now, WHY would I have switched from a Berendsen temperature-coupling algorithm to the V-rescale algorithm? Because of this cautionary note that I started receiving in GROMACS 4.5 when I started the position-restrained mdrun: NOTE 1 [file pr.mdp]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. I took this as a warning that a deeper study of the algorithms had revealed a flaw in Berendsen, and so I sought to use what GROMACS was advising me would be a better choice. This is apparently MISLEADING advice when doing the initial equilibration. If you are using the Berendsen pressure algorithm, you must also use the Berendsen temperature algorithm. I know that mdrun cannot be sophisticated enough to know which phase of my run I am performing, but I hope that the GROMACS documentation will be revised to discuss the appropriate use of the V-rescale thermostat. I just misused it,and wasted a lot of time as a consequence. I hope that some discussion of its proper use would be written and summarized on a page like, for example, this one: http://www.gromacs.org/Documentation/Terminology/Equilibration It already states: "Using, i.e., the Nosé-Hoover thermostat for initial NVT equilibration can lead to wild oscillations of the temperature, with the system ultimately blowing up." A similar warning should be added about the V-rescale thermostat in NPT equilibration, ESPECIALLY if GROMACS is going to issue messages that recommend that you use it! There is a page for the Berendsen barostat/thermostat: http://www.gromacs.org/Documentation/Terminology/Berendsen There is apparently no corresponding page for the V-rescale thermostat. Perhaps one should be written. -- View this message in context: http://gromacs.5086.n6.nabble.com/Re-Water-molecules-cannot-be-settled-why-tp4999302p5001121.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
