AMBER Archive (2004)

Subject: Re: AMBER: rms in ptraj

From: Thomas E. Cheatham, III (
Date: Mon Jan 05 2004 - 10:04:20 CST

> Please anyone can tell me how does the time interval work in the rms of ptraj.
> If I have run an MD with 1ns with ntwx=100 so I have got one mdcrd with 10000
> frames.If I want to get the rms of them just correspond to the 10000 frames,
> should I set the time interval with 1 or 100? Thanks in advance.

The time interval is in picoseconds; so, if you write the coordinates
every 100 steps (assuming a 2 fs time step), the time would be 0.2; if you
are running with a 1 fs time step, the time would be 0.1.

rms first time 0.2 @CA out rms.backbone

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