[AMBER] REMD_suggestion

From: Thakur, Abhishek <axt651.miami.edu>
Date: Wed, 18 Jan 2017 15:03:26 +0000

Hi everyone,

I need some suggestion, in my project I am running MD in implicit water model for around 1200ns. My protein is a dimer and I am expecting my dimer to open. But as till now I have not observed such thing so I am planning to for Replica exchange MD.

I have never done it before, so I have few questions regarding that

1. Is it ok to run REMD in implicit water model?

2. As I am expecting long run can I use dt=0.04 after Hrepartitioning the prmtop file?

3. Except SMD is there anything else that I can give it a try?

4. Earlier I have used ntt=1 I have observed my dimer to separate just after 20ns but now using ntt=3 I am not observing much change.

Will be thankful for your suggestion.

With regards,

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Received on Wed Jan 18 2017 - 07:30:03 PST
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