[gmx-users] lincs errors late in simulation

Mark Abraham mark.j.abraham at gmail.com
Tue May 14 18:11:01 CEST 2013

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.

On May 14, 2013 4:28 PM, "Joe Smerdon" <JSmerdon at uclan.ac.uk> 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
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