[gmx-users] How to implement dihedral restraints

Mark Abraham Mark.Abraham at anu.edu.au
Thu Dec 14 00:36:20 CET 2006

chris.neale at utoronto.ca wrote:
>> For example, my peptide is rotating 50 degrees about a bond B-C, out 
>> of four
>> bonded atoms A-B-C-D.  I want to apply additional force on this
>> dihedral(B-C) during my simulation(only for this particular atoms to 
>> make it
>> rotate further till 180 degrees). All the remaining atoms in the peptide
>> will have normal force as usual.
>> May I ask you, how can I apply this in gromacs code.
>> Any help will be appreciated!
> The current manual is good at describing what the options do for  
> dihedral restraints, but (to my knowlegde) doesn't explain at all how  
> to get the implementation up and running. Here is how I have done it  
> based on searching the mailing list for answers. I suggest that  
> something like this is added by way of example to the manual for  future 
> releases.
> Also, the manual is a bit unclear about whether this type of dihedral  
> restraint is stable for use near 180deg. I have found that for my  
> system everything appears to behave normally and as expected over the  
> entire range of dihedral angles including 180deg.

Well that seems fortuitous, since I can't see anything in Chapter four 
that suggests that these restraints should be stable around 180 degrees. 
Perhaps there are other dihedrals along B-C that are not around 180 
degrees that will be safer to couple?


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