On Thu, Feb 11, 2016 at 3:24 PM, Batuhan Kav <bkav13.ku.edu.tr> wrote:
> Hi Dan,
>
> Thank you for the reply. Yes, I did check via parmed and it showed me the
> error in the topology file.
>
> I’m not sure if this is relevant but what might be the reason that sander
> did not complain about the topology while minimising and heating the
> system, but it halted when the equilibration started?
>
The part of the prmtop file that is corrupted is the definitions of which
atoms belong to molecules. In short, sander relies on the prmtop to tell
it which atoms are all connected by bonds. The only thing that sander
*does* with this information is scale the COM of each molecule during a
constant pressure simulation. So if you have a prmtop where the molecule
information is incorrect, it will work fine for NVT or NVE calculations,
but may lead to unpredictable behavior as soon as you move to NpT (which is
typically what one does first for "equilibration").
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Feb 11 2016 - 13:00:03 PST
