Re: [AMBER] How to use the ntb options in amber-cuda-version

From: <>
Date: Tue, 1 Sep 2020 16:34:08 +0800

   Hello professor, thanks so much for your kind replies! Now, I know how I
   shoud do. I had really learned much from your suggestions.
   Best wishes!
   Ning Wang

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   On 09/01/2020 15:39, [2]David Cerutti wrote:

     As stated on page 360 of the Amber20 manual, ntb = 1 stipulates constant
     volume conditions, ntb = 2 constant pressure. If ntb == 2, you must have
     some sort of barostat working ("barostat" keyword). There is one more
     wrinkle here: if you want isotropic box size rescaling (which is
     appropriate for proteins in water), specify ntp = 1. Otherwise specify
     = 2 for anisotropic rescaling in systems like crystal lattices. There is
     even semi-isotropic rescaling (equal proportions in X and Y, independent
     proportion in Z) for membrane simulations, where you have a system that is
     reasonably isotropic in two dimensions (the lipid bilayer) and a third
     dimension that should not be coupled to the other two.
     You are correct about the equilibration protocol, and that the production
     MD should occur at constant pressure in order to measure Gibbs free
     You should do your initial 100-200ps of constant pressure MD in the CPU
     code, unless you are confident you have added enough water to maintain the
     volume you started with (which would probably also take a program like
     AddToBox or CHARMM-GUI rather than the tleap water box tiling procedure).
     I would recommend at least 10ns in NVT, with positional restraints on key
     atoms, before you move on to the NPT step. The NPT can still have some
     positional restraints, but make sure they are light (0.1 kcal/mol-A2) by
     the time you start this. Start the restraints off at 1-5 kcal/mol (or
     more), then ramp 'em down to the 0.1 range to start NPT. (Note that you
     use the CUDA code for the NVT part, then swap to the CPU code briefly,
     back to the CUDA code.) I would advise CPU code for the initial energy
     minimization, too: the GPU code does some sophisticated things with its
     precision format in order to make energy minimization possible, but just
     understand that we had to go to some lengths in order to make it
     safe. Safer still to just let the CPU work for five minutes on that
     Good luck!
     On Tue, Sep 1, 2020 at 2:33 AM <> wrote:
> Hello, Amber users!
> Recently, I want to empoly Amber program packages to simulate a
> protein in water system in order to guide my wet experiments. I plan to
> the cuda-version of Amber18 to run. But I had mentioned some tips from
> amber18 manual that was "Avoid using the NPT ensemble (ntb=2) when it is
> not required; if needed make use of the Monte Carlo barostat
> Performance will generally be NVE>NVT>NPT (NVT~NPT for barostat=2)." In
> knowledges, the protein-salt-water system was should be considered to
> simulate under the npt ensemble for final MD production. So, I'm
> whether to chose the option ntb=1 or ntb=2. I known that the
> protein-salt-water simualtion should be equilibrated by NVT and NPT
> ensemble before MD production. So, How should I process the simulation
> with amber18 cuda version. Please help me. Any suggestion is welcome.
> Best wishes!
> Ning Wang
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Received on Tue Sep 01 2020 - 02:00:02 PDT
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