Re: Does "rigidbond off" work instead of "rigidbonds none"

From: Leonardo Trabuco (ltrabuco_at_ks.uiuc.edu)
Date: Fri Sep 03 2010 - 01:21:01 CDT

Dear Mert,

On Thu, Sep 2, 2010 at 10:03 PM, Mert Gür <gurmert_at_gmail.com> wrote:
> Dear all,
> This question is just out of curiosity.
>
> One of my friends did a long MD simulation writing "rigidbonds off" in
> the configuration file.
> However in the user guide it says that
>
> Acceptable Values: none, water, all
>
> My friends MD simulation have run for a long time.
>
> Does using  "rigidbonds off" mean  "rigidbonds none"?
> If so could I use "off" for any of the "none" values in the configuration file?
> If it does not mean "rigidbonds none" how can I check what it actually did?

Have you looked at the log file? Something like:

Info: RIGID BONDS TO HYDROGEN : WATER
(...)

Cheers,
Leo

> I am asking these questions because I am planning to use the resulting
> trajectory for further analysis (TMD and SMD).
>
> Best,
> Mert
>
>

--
Leonardo Trabuco, Ph.D.
CellNetworks, BioQuant
University of Heidelberg, Germany

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