Re: [AMBER] Imaging issue in DNA - cpptraj

From: Satyaseelan C <bo17resch11006.iith.ac.in>
Date: Fri, 4 Dec 2020 23:17:10 +0530

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

Thanks & Regards
Sathyaseelan

On Wed, 2 Dec, 2020, 7:25 PM David A Case, <david.case.rutgers.edu> 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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Received on Fri Dec 04 2020 - 10:00:02 PST