[gmx-users] Rigid body optimization

Anton Feenstra feenstra at chem.vu.nl
Thu Dec 4 09:14:02 CET 2003

Matthew Hotchko wrote:
> I sent a similar message and no one replied.  I guess that means no one 
> knows the answer.  Just in case you missed it, here I go again.  

Strange, I did send a reply. I'll paste the answer back in again,
and add some additional thoughts that have occurred to me...

> I am trying to use Gromacs to analyze multiple configurations of a two 
> protein complex.  I would like to set the structures with rigid bonds and 
> rigid angles, to make both of the proteins rigid bodies.  I tried using 
> constraints         =  all-angles
> in my md simulation .mdp file, but when I run grompp, I get the following 
> error.  
> Fatal error: No bond information for bond H1-N or N-H2

constraints = all-angles is not often used, so you may have stumbled on
a bug here. Could anyone confirm whether all-angles constraints still
works (and with which FF's it works), or confirm that it indeed is shaky?

Another thing is that this does *not* make your protein really rigid,
just more rigid than it normally would be. There is no proper 'rigid body'
constraints algorithm implemented in Gromacs...

> Secondly, I would like to do a different MD simulation where only the 
> energy of the protein-protein interfaces/interactions is counted.  I have 
> two proteins, labled chain E and chain I.  I made an index file for these 
> two residues and then tried using the 
> energygrp_excl     =  chE chI
> energygrps          =  chE  chI

IIRC, energygrp_excl expects group *pairs*, and you'd want to exclude only
the self interactions, like:
energygrp_excl = chE chE chI chI

The other line you could leave as it is.


  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |

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