Re: [AMBER] Saving trajectories with ntwprt

From: Jason Swails <>
Date: Fri, 13 Nov 2015 08:29:57 -0500

On Fri, Nov 13, 2015 at 8:25 AM, Batuhan Kav <> wrote:

> Dear All,
> I am simulating a system of two monomers in explicit water box. I will
> obtain long trajectories (around 500-1000ns) so I want to reduce the
> size of the mdcrd file. For that, I use ntwprt option and save only the
> monomer atoms. However, as a part of my calculations, I will need the
> water molecules that are close to monomers. I wonder if there is a way
> to save solvent molecules which are, say 5 A, close to the monomers, or
> the solvent molecules in the first-second solvation shells.

‚ÄčNo, it is not possible.

As for reducing the size of your trajectory files, try using ioutfm=1
(NetCDF files). These are typically a fraction of the size of ASCII mdcrd
files. They are also faster to read and write, they are more fault
tolerant, and store positions in higher precision.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Fri Nov 13 2015 - 05:30:06 PST
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