Re: [AMBER] RMS is zero

From: Stephan Schott <>
Date: Tue, 4 Sep 2018 22:58:04 +0200

Hi Hadi,
The issue is that rms by default makes a best rms fit. To avoid this, add
nofit to your command. Also, if you want to make an rms fit to a reference,
you have to specify this instead of first. You can check the options of
different commands with " help <command> ".
Hope it helps,

El mar., 4 sept. 2018 a las 22:36, Hadi Rahmaninejad (<>)

> Hello Ambe Users,
> I am calculating rms of a single atom (Methane) in a system. There are some
> atoms which I made them fix using "ibelly", but not the methane. When I
> visualize methane with vmd it is clearly moving. However, when I am
> calculating the rms using cpptraj program, the output is zero. the command
> for cpptraj which I used is like below:
> trajin
> reference 02_Heat.rst
> rms first out 03.rms :4201.ME
> I highly appreciate if you have any suggestion.
> Thank you in advance,
> Hadi
> _______________________________________________
> AMBER mailing list

Stephan Schott Verdugo
Heinrich-Heine-Universitaet Duesseldorf
Institut fuer Pharm. und Med. Chemie
Universitaetsstr. 1
40225 Duesseldorf
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Received on Tue Sep 04 2018 - 14:00:02 PDT
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