From: Kevin C Chan (cchan2242-c_at_my.cityu.edu.hk)
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.
On Tue, Apr 18, 2017 at 10:37 PM, <nikolaev_at_spbau.ru> 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
> 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,
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