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

Dastmalchi dastmalchi.s at tbzmed.ac.ir
Mon Dec 27 08:22:34 CET 2004

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?
## 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?

Thanks for your kind help.

Cheers, Siavoush

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