RE: [AMBER] production phase

From: Ross Walker <>
Date: Fri, 17 Jul 2009 04:56:13 +0100

Hi Bill,

> In AMBER tutorials, I found the author used ntb=1 with NTT=3, ntb=2
> with NTT=3 or ntb=1 with NTT=1 in production phase.
> which condisiton we should use in the production phase, constant volume
> or constant pressure?
> Also, the author used NTT=1 in place of NTT=3 just to savetime only,
> but NTT=3 is prefered than NTT=1, didn't he?

This is not as simple a question as you think it is. It depends on what you want to simulate, what you want to learn etc. Generally I recommend heating with ntb=1, ntt=3 then equilibrating the pressure with ntb=2,ntt=3 and then switching to constant volume (ntb=1) for production at which point you can either keep a langevin thermostat, if you want langevin dynamics, switch to ntt=0 and run NVE=0 or use a very week berendsen coupling ntt=1.

Be aware that Langevin is more expensive in parallel since it does not scale as well. NTT=3 necessarily corrupts the dynamics so if you want to measure things like correlation functions you will not be able to do this with ntt=3. So it really is a question of what you are actually looking to simulate.

All the best

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
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Received on Fri Jul 17 2009 - 01:08:39 PDT
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