Re: "the error of movement of atoms"

From: Brian Radak (
Date: Fri Mar 01 2019 - 16:17:57 CST

I would recommend against lots of minimization. For a well prepared
structure 200 - 1000 cycles should be more than enough (I've never done
more than 200 in all of my years using NAMD). A large number of steps can
cause trouble with periodic boundaries (something with the patch updates?).
You can also try increasing margin (5 usually works for me) during the
initial constant pressure equilibration and then set it back to the default
(overall performance might be bad otherwise).

On Fri, Mar 1, 2019 at 4:05 PM soroush ziaei <>

> hello everybody,
> At first, I have to say the number of atoms of my simulation is 140000.
> And after running the first stage of simulation that means minimization at
> 10000 steps in order to check the error before running a full simulation,
> but at the next stage ( temp & pressure coupling ) an error appears in the
> log file that says some of the atoms with related numbers are unstable and
> moving too fast, why?
> I think it's because of the short time of minimization, am I right? if
> not, please guide me.
> Regards,
> soroush

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