[gmx-users] How to implement dihedral restraints
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
> 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?
More information about the gromacs.org_gmx-users