[AMBER] Replacing water with a H2O2 and restart the simulation

From: Morteza Chehel Amirani <morteza.amirani.gmail.com>
Date: Thu, 26 May 2016 16:21:16 -0600


I have a simulation which was running for 10 ns. Now, I want to replace one
of water molecules with a hydrogen peroxidase. I'm wondering what the best
way is to kind of restart the simulation?
Do I need to prepare the topology file from the scratch, or I can make a
new topology file only for the peroxide and combine it with the original

In the case I make the a new topology file for the new system, how can I
import the simulation box information into it?

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Received on Thu May 26 2016 - 15:30:03 PDT
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