I wouldn't call 8ps "late." Since you probably don't know how large a time step is safe, I'd try 0.1 fs for equilibration, and raise it later if it proves stable.
Mark On May 14, 2013 4:28 PM, "Joe Smerdon" <[email protected]> wrote: > > Hi all, > > First of all I'm new to md simulations, so if I am missing anything > simple, I would be grateful for any pointers, however small. I am trying > to simulate many small molecules on a substrate. I am restraining my > substrate from moving but allowing the molecules to do whatever they like. > My steps are to minimise my system (136 molecules on a 200Ax200A surface > of about 4 layers, with 100A vacuum), then to run an NVT simulation without > pbcs (though I could use pbcs, I just don't really need to for this). I am > getting LINCS errors late on in the simulations - they don't always cause a > crash, but sometimes they do. I guess it can't be insufficient > minimisation if the errors arise after the simulation has been underway for > awhile (eg, step 15000, 8ps into a 50ps simulation), but I don't really > know what it can be. My timestep is 0.5 fs. I am just experimenting at > the moment, I intend to simulate for much longer when I get it working. > > I guess my question is: are LINCS errors that occur late in a simulation > due to poor minimisation, or not? If not, what other factors should I look > at? > > thanks > > Joe > > -- > gmx-users mailing list [email protected] > 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 [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
