On Fri, Jan 30, 2015 at 3:29 AM, Tong Zhu <tongzhu9110.gmail.com> 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.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Jan 30 2015 - 01:30:04 PST
