Dear Amber users,
I'm planning to run a large implicit solvent simulation of myosin using AMBER 12. I had a few questions that I was hoping someone could help me with.
1 - The molecule is quite big and I plan to use GPU's. The tutorials i looked at use a Langevin thermostat, but the GPU page states that this is very inefficient and I should use the Berendsen or Anderson thermostats. As the AMBER manual rules out the Berendsen due to issues with implicit solvent model, I guess I'm stuck with the Anderson (ntt=2). Could anyone with experience let me know the best setting for vrand (other than the default of 1000?) From what I've read this is the only variable associated with the Anderson thermostat?
2 - What settings do people use to equilibrate an implicit solvent simulation? Is the only consideration increasing the temperature from 0K to the target temp?
3 - Parts of the structure I'm using has been homology modelled. Are there any established protocols that anyone is aware of that I could use to test the stability of my structure?
Thanks in advance,
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Received on Wed Mar 25 2015 - 17:00:02 PDT
