Re: [AMBER] Saving trajectories with ntwprt

From: Jason Swails <jason.swails.gmail.com>
Date: Fri, 13 Nov 2015 08:29:57 -0500

On Fri, Nov 13, 2015 at 8:25 AM, Batuhan Kav <bkav13.ku.edu.tr> 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.

HTH,
Jason

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