[gmx-users] how to constrain a solvent different from water

ying-hua-chung at uiowa.edu ying-hua-chung at uiowa.edu
Sat Dec 25 01:49:32 CET 2004

I am trying to do a simulation of hydrogen peroxide, water, and protein.
I would like to use spc for water and opls for the protein. That is easy, but 
I also want to build an itp file for hydrogen peroxide in which bonds and 
angles are constrained but not the dihedral angle.
I am not sure of how to set up the constraints.
If I say in the mdp file constraints "none" can i still use a constraint 
section in the itp file? 
If I say something else in the mdp file then my protein will also get 
constraints ...

Can I use lincs or shake to do this? If so should i only worry about the itp 
file or do i need to do anything with my mdp file?

The only example I see of this is the various flavors of water (spc, tip4p, 
etc) in the top directory, but those are handled with settle which seems to be 
a non-standard procedure. How should the constraint section look like for 
something that has 4 atoms instead of 3 like my hydrogen peroxide?
Does anyone have any itp example to share related to this?

Thanks for your help!!! I am new at this ...


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