Re: Segmentation fault during water MD

From: Kevin C Chan (
Date: Tue Apr 25 2017 - 06:59:07 CDT

You might consider looking at a plot of energy during minimization, see if
it went to a plateau. The suitable number of minimization steps depends on
the size of your system, so it can be MUCH larger than you expected.

CityU HK

On Tue, Apr 18, 2017 at 10:37 PM, <> wrote:

> Dear all,
> I am trying to equilibrate my protein. On one step I put it into the water
> box, run the molecular dynamics of water molecules with protein fixed.
> Then I release all residues which are within 8A of chromophore (all other
> atoms fixed), and perform energy minimization for 500 steps. Then I try to
> run equilibration of water again: 1000 minimization steps and then 5000
> MD.
> However, on the last stage when MD of water starts, Segmentation fault
> happens. No error is written.
> What can be the problem?
> Thank you in advance,
> Dmitrii.

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