hi
On Wed, Jan 18, 2017 at 10:03 AM, Thakur, Abhishek <axt651.miami.edu> wrote:
> 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?
>
1 and 2: indeed. We did run REMD in implicit solvent (igb=8) with dt 4fs
after H-mass stuff (from 1-30 microsecond per replica).
http://pubs.acs.org/doi/full/10.1021/ja5032776
>
> 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.
>
It's hard to tell. What happens if you ran 10 MDs with ntt=1 and 10 MDs
with ntt=3?
Hai
>
>
> Will be thankful for your suggestion.
>
>
> With regards,
>
> -AT
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Received on Wed Jan 18 2017 - 09:00:03 PST
