AMBER Archive (2003)

Subject: Re: Protein - DNA complex simulation - protocol

From: Pratul Agarwal (pratulka_at_rocketmail.com)
Date: Tue Apr 29 2003 - 09:39:18 CDT

Few suggestions:

1. If I understood it correctly, you raised the system temperature
    to 300K during a constant pressure MD. I have had problem doing
    this. In my case the system expanded too much, which ultimately
    lead to SHAKE problems later. I fixed this my raising the system
    temperature during a constant volume run and then did a constant
    pressure run.

2. What is the step size are you using for MD? In my system there are
     close interactions between the protein and DNA and the atoms kept
     coming too close with a step size of 2 fs. I found a step size of 1 fs
     appropriate.

3. If nothing else works, you could also try more steps in the initial
     minimizations.

4. Regarding the solvent moving out of the box, is this after "imaging"
     the system?

Good luck.

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