[gmx-users] Blowing Up - intramolecular energy terms

[Liz Bell]

Dear all,


Is there a possibility to plot the intramolecular energy terms?

 

3. of "Diagnosing an Unstable System" of the page

 

http://www.gromacs.org/Documentation/Terminology/Blowing_Up

 

sounds as if this is possible. Gmx energy only shows the non bonded interaction energys of the energy groups but not of the energy terms like

angle or dihedrals

 

I found the Dihedral PCA part

http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA

which enables such a calculation of the energy of the dihedrals.

 

But what about the bonds or angles?

Is there also a posiibility to plot those energy terms?

Any idea?
 



Tank you very much in advance.
Best,

Liz





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Re: [gmx-users] Blowing Up - intramolecular energy terms

[Mark Abraham]

Hi,

Total bonds and angles are already available in the .log and .edr files. If
some component is blowing up, so will the total.

Mark

On Mon, Sep 7, 2015 at 6:51 PM Liz Bell  wrote:

> Dear all,
> Is there a possibility to plot the intramolecular energy terms?
>
> 3. of "Diagnosing an Unstable System" of the page
>
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up
>
> sounds as if this is possible. Gmx energy only shows the non bonded
> interaction energys of the energy groups but not of the energy terms like
> angle or dihedrals
>
> I found the Dihedral PCA part
> http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA
> which enables such a calculation of the energy of the dihedrals.
>
> But what about the bonds or angles?
> Is there also a posiibility to plot those energy terms?
> Any idea?
>
> Tank you very much in advance.
> Best,
> Liz
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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