[gmx-users] couple of questions about H-bonds and constraints

Ran Friedman ran at hemi.tau.ac.il
Mon Dec 27 16:28:55 CET 2004


Dastmalchi wrote:

> Hi there,
> 1) I want to keep the secondary structure conformations in different 
> parts of my protein structure fixed, say for example, residues 20-40, 
> 60-80, and 90-100 needs to be remained in helical conformation during 
> the MD simulation. I would have thought that constraining the hydrogen 
> bonds will do the job, so I was experimenting on a small helical 
> peptide and put "Constraints = hbonds" in the md.mdp file. However, 
> during a short MD the peptide did not keep its helical conformation 
> and the number of h-bonds was changing during the MD.
> ## Is this the right way for fixing the secondary structure?

No. Constraints = hbonds will constrain the length of bonds containing 
hydrogen atoms.

> ## Maybe I need to set some kind of force constant for this to happen. 
> Is that right?
> ## As I mentioned above I want this in different parts of protein. Do 
> I need to assign these parts different groups and somehow tell the 
> Constraints = hbonds to just apply the constraints on these groups?
> ## How can I assign different parts as different groups?
> 2) How can I apply the "Define = -DPOSERS" to different parts in the 
> structure?

I think that the simplest solution to your problem will be to edit the 
posre file.

> Thanks for your kind help.
> Cheers, Siavoush
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