I try the following: 0. Minimization 1. NVT (100,000 steps of 2fs, 300K) 2. NPT (100,000 steps of 2fs, 300K, V-rescale thermostat) 3. NPT (5000 steps of 2fs, 308K, V-rescale thermostat) 4. 9 x NVE (each 32768 steps of 0.75 fs) 5. go to step 3.
I plan to get rid of the first of nine NVE steps, as an NVE equilibration step. At 0.75 fs, the total energy drop was about 0.03% per NVE step. Will that be fine? I am a bit worry that step 3 is too short. I pick 308K because last time when I choose 300K for step 3, step 4 drops to 292 K. I hope that the NVE will be about 300K. May be I should look at the .edr file of step 3. Thanks. On Wed, Sep 3, 2014 at 11:54 AM, Johnny Lu <johnny.lu...@gmail.com> wrote: > reading this post in maillist again: > https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2012-May/071225.html > > I think that is exactly the same problem. > > > On Wed, Sep 3, 2014 at 10:24 AM, Johnny Lu <johnny.lu...@gmail.com> wrote: > >> Hi. >> >> After equilibrating with NVT (for 10,000 steps of 2fs) and then NPT >> (10,000 steps of 2fs with V-rescale thermostat at 300K), when I run NVE >> (0.5fs timesteps) with a harmonic restraint with force constant 4184kJ/mol >> rad^2, the temperature then fluctuate around 292 K ( >> http://oi60.tinypic.com/sni5at.jpg) in gromacs 4.6.6. >> >> When I instead run NVE with same setting except without the constraint >> after the two equilibration steps, the temperature stays around 300K. >> >> What is the cause of this drop of temperature to 292K? >> >> Thanks again. >> >> >> > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.