[gmx-users] Constraints specified in .mdp as well as in .top files

Berk Hess gmx3 at hotmail.com
Mon May 18 11:07:17 CEST 2009


I think the manual is pretty clear on this:
No constraints except for those defined explicitly in the topology, i.e. bonds are represented
by a harmonic (or other) potential or a Morse potential (depending on the
setting of morse) and angles by a harmonic (or other) potential.


> Date: Sat, 16 May 2009 12:04:09 +1000
> From: Mark.Abraham at anu.edu.au
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Constraints specified in .mdp as well as in .top files
> Vishwanath Dalvi wrote:
> > Thank you for your response.  I am still unclear as to how the whole 
> > thing works (and the manual is no help). 
> > 
> > If I do specify (in the .mdp file) something like constraints = 
> > all-bonds, will that override the harmonic-bond interactions specified 
> > in the .itp files? 
> Don't know. Check the manual, or try it and see. Either your .log file 
> output or inspection of gmxdump of your .tpr might be useful here.
> Mark
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