Re: [AMBER] Imaging issue in DNA - cpptraj

From: David A Case <>
Date: Wed, 2 Dec 2020 08:55:09 -0500

On Wed, Dec 02, 2020, lomzov wrote:

>1) as suggested by Anselm using iwrap = 0, but for long-term simulations
>(more than 50-100 ns) water molecules and cations may go too far and
>this cannot be written to the old format mdcrd file.

The expectation is that you will use netcdf format for trajectory and
restart files. If you need the old format mdcrd for something, then
do this in cpptraj:

      read in the netcdf trajectory
      image the water ions
      write out the trajectory in mdcrd format

...good luck...dac

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Received on Wed Dec 02 2020 - 06:00:05 PST
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