O.K Chris Thanks for all your help. I am actually considering removing the thermostat all together seeing as my system is quite small. I have also started using gen_vel = yes (no matter how much I think my system is in equilibrium). One quick question (perhaps its silly). When you say the initial forces become the initial velocities; I thought the initial velocities were taken from the velocities in the initial configuration (taking into account that I do have velocities in the initial configurations from previous simulations).
Cheers Gavin chris.ne...@utoronto.ca wrote: > Gavin, I recall mentioning gen_vel=no with temperature coupling as a > possible problem a while ago (the problem is that the initial forces > become initial velocities and then those get scaled up and what you > have are velocities and not temperatures -- read about the flying ice > cube problem). Do you have any idea why it would only cause you > problems at a distance of greater than 2 nm? > > Also, Justin seemed to intuit this was a thermostat. I suspect that if > you switch to the sd integrator things will all be ok. I don't really > do anything in vacuum so it was harder to pick this up. > > If you're tied to your md/NH settings, then you probably need to > reduce the timestep -- but you will probaby run into problem > eventually here too so I don't advise it. > > Chris. > > -- original message -- > > Dear Chris and Justin > > I ran a simulation for two water molecules (100 ns). It only took 5 > minutes. Firstly I ran the simulation with ref distance 2.35 nm, genvel > =yes, and gen temp =600 (using Nose Hoover). This produced a histogram > with one main peak. I then took the final configuration from that > simulation and ran the simulation again for the exact same duration and > parameters etc, with the only exception that I set gen_vel = no. The > resulting histogram did indeed have two main peaks. I am now currently > running the simulation of my two cage molecules using berensden > thermostat to see if there is a difference. > > Many Thanks > > Gavin > > > -- 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/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/mailing_lists/users.php
