Re: [AMBER] big cavity in the trajectory

From: Jason Swails <>
Date: Fri, 30 Jan 2015 04:04:25 -0500

On Fri, Jan 30, 2015 at 3:29 AM, Tong Zhu <> wrote:

> Dear amber users,
> I want to image my trajectory to the original box using cpptraj. The input
> file is :
> trajin ch2o_prod_v0_l0.crd 1 30000 30
> center :1 origin
> reference ch2o.rst
> center :1
> image center familiar
> rms reference :1 out backbone_rmsd_ppc.dat
> trajout image.crd
> However, I found a great cavity (without any water molecules) in the imaged
> trajectory (please see the attached picture). Could you please tell me how
> can I fix this problem?

​Run a constant pressure simulation to equilibrate the system size (and
density). The starting box size that LEaP assigns is much too large,
resulting in the equivalent of a very low external pressure​

​in constant volume simulations, leading to the simulation "boiling", as
you noticed here.

In my experience, once your simulation gets to this point, it takes a long
time to squeeze out the bubble using a barostat. The best idea would be to
run a very short heating in constant volume following the initial
minimization (like 50 ps, for instance), then switch to running constant
pressure MD until the density stabilizes.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Fri Jan 30 2015 - 01:30:04 PST
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