Justin Lemkul wrote > So the initial equilibration was NPT? Yes.
Justin Lemkul wrote > Did you ever try simply running NVT with > either Berendsen or V-rescale before applying any type of pressure > coupling? No, I haven't, and I don't remember seeing that described in any work flow. Justin Lemkul wrote > Immediate application of NPT is often unstable for a variety of reasons, > not > necessarily the temperature coupling algorithm. All right, that's useful information. But what I am doing here is ripped from a tutorial file, and modified as little as possible. I try not to change things that I do not yet understand. My source for the MDP files was the lysozyme tutorial shell script that accompanied GROMACS 3.3. If there are procedures in that tutorial that are obsolete, I guess I'm finding that out the hard way. Justin Lemkul wrote > Anyone is welcome to contribute to the wiki; it is a community project, > after > all. I would also be interested to see if it can be demonstrated that NPT > with > V-rescale + Berendsen is unstable after an independent NVT simulation with > either method. I may take the time to try that experiment later. I'll report back with any findings. Thanks for your help! -- View this message in context: http://gromacs.5086.n6.nabble.com/Re-Water-molecules-cannot-be-settled-why-tp4999302p5001131.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
