Re: [AMBER] unwrap problem in the liquid water dynamics trajectory analysis

From: jinfeng liu <>
Date: Mon, 17 Sep 2018 09:47:44 +0800

Dear David,

      Thanks for your reply.

The size of periodic box is:15.1133247 15.9353031 15.6238333. Because the
atomic forces are calculated by QM method, and then we replace the amber
forces with these QM forces during the MD simulation. So the size of the
system is not large, because of the expensive QM calculation.

I want to make sure each water molecule is in the primary unit cell during
the simulation, so the iwrap=1 is used.


David A Case <> 於 2018年9月17日 週一 上午8:59寫道:

> On Sun, Sep 16, 2018, jinfeng liu wrote:
> >
> > Recently I performed liquid water dynamics under the periodic
> > boundary condition in the NVT ensemble using the "iwrap=1". The unit cell
> > of water box contains 128 SPC/FW water molecules. I need to remove the
> > effect of "iwrap=1" in the trajectory before the diffusion coefficient is
> > calculated.
> To add to the good comments earlier:
> 1. I'm a little surprised you can even do a calculation with just 128
> water molecules. You would certainly need more to avoid bad effects
> from artificial periodicity. What is the size of your periodic box?
> 2. For diffusion (and for other dynamic parameters) you need to run NVE
> simulations (following equilibration in NPT). Thermostats inevitably
> interrupt Newton's equations, and destroy the very time-dependent
> behavior you are trying to measure.
> 3. Why use iwrap=1 at all?
> 4. As noted earlier, be sure you are using SPC/FW correctly. You need
> to add "set default FlexibleWater on" in your leap input.
> ...good luck...dac
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Received on Sun Sep 16 2018 - 19:00:02 PDT
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