Re: [AMBER] Simulation does not restart from restart file written in previous step.

From: Abhilash J <>
Date: Thu, 8 Mar 2018 18:01:25 +0530


   I did use iwrap=1 in this simulation.
   After having a look at the structure of complex with water at end of the
last frame of the simulated trajectory, iwrap=1 does look as the most
probable cause.


On Wed, Mar 7, 2018 at 7:22 PM, David A Case <> wrote:

> On Wed, Mar 07, 2018, Abhilash J wrote:
> >
> > Thanks, Ruchika and Case for the help.
> > Last restart file showed ligand far from the protein cavity.
> > making a new restart file using autoimage command solved the issue.
> Not sure if this is relevant or not: you should not use iwrap=1 in
> simulations like this, since it may have been wrapping that caused the
> symptoms you reported. [Of course, ignore this if you were not using
> wrapping.]
> (Regular readers of this list know that I think there are no types of
> simulation where iwrap=1 is appropriate.)
> ....dac
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Received on Thu Mar 08 2018 - 05:00:03 PST
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