AMBER Archive (2009)

Subject: Re: [AMBER] combining MD runs for post-MD analysis

From: Bill Ross (
Date: Mon Sep 21 2009 - 12:32:53 CDT

> I have completed two MD runs based on the same topology file:
> 1) MD1 : from 1ps to 2000ps
> 2) MD2 : from 2001ps to 4000ps
> Currently I have 2 separate sets of results (e.g. mdcrd=2C etc) from those =
> two MD runs.=A0
> Is there a way to combine the separate sets of results before I start my po=
> st-MD analyses (e.g. RMSD=2C MM/PBSA=2C etc)? Will cat md1.mdcrd md2.mdcrd =
> work?

If it's all production (after NVT and NPT equilibration) you could
use ptraj to join the trajectories. They can't be catted together;
if you 'head <file>' you will see why and what it would take to
combine using other tools if desirable.


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