[AMBER] Saving trajectories with ntwprt

From: Batuhan Kav <bkav13.ku.edu.tr>
Date: Fri, 13 Nov 2015 14:25:02 +0100

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.

All the best,

AMBER mailing list
Received on Fri Nov 13 2015 - 05:30:05 PST
Custom Search