Re: [AMBER] Imaging issue in DNA - cpptraj

From: Satyaseelan C <>
Date: Fri, 4 Dec 2020 23:17:10 +0530

Thank you sir for your suggestion. I will follow the above mentioned steps

Thanks & Regards

On Wed, 2 Dec, 2020, 7:25 PM David A Case, <> wrote:

> 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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