[gmx-users] fitting dihedral angle function parameters using gromacs
fay4 at pitt.edu
fay4 at pitt.edu
Sun Jan 24 02:30:27 CET 2010
Dear Mr. Chris:
Thanks for your reply! I will try your method!
> I have never done this myself. Nevertheless, I'm going to take a shot
> since you haven't got an answer yet.
> Dihedral parameters can be thought of as consistently developed fudge
> factors that are used to fine-tune a parameter set. The word
> consistent here implies that there is a method to developing them that
> is specific to each forcefield and you should follow that method.
> Therefore everything that I say here is only useful in terms of
> helping you to get an idea of what these 3 steps might look like and
> not necessarily what they should look like in your particular case.
> I call dihedrals fudge factors since they don't imply anything of any
> physical relevance in and of themselves when you have explicit
> hydrogens. For example, the emphasis that they may place on staggered
> conformations of sp3 carbons might be able to come out of the NB LJ
> parameters directly if those parameters weren't representing some type
> of convoluted average over different interaction types (which they
> likely are). For united atom ff's the dihedrals likely do represent
> something of physical relevance... the hydrogens.
> Step 2 is easy. Simply set the dihedral parameters to zero and run
> some MD simulation. I suspect that you can do this in vacuum, but
> again that depends on your forcefield. The ab initio calculations are
> done in vacuum so I don't see why this step would need any solvent.
> Step 3 would start with calculating the probability of dihedral angle
> value occurrence as a function of dihedral angle value by
> histogramming your MD sampling. You can then turn this into a free
> energy by E=-KbT*ln(P). You then look back at your results from step 1
> and figure out the dihedral function that should be applied on top of
> the free energy profile that you get in step 2 in order to (we hope)
> give you the conformational preference that you desire out of your MD
> simulations. This of course would require that you did ab initio
> calculations for multiple dihedral rotamers so that you know the
> relative energies (and therefore probabilites of occurrence) of each.
> Note that different force fields put emphasis on different things. For
> example, I believe that the CHARMM ff puts as it's number one priority
> the ability to reproduce actual experimental values. Therefore in this
> case, you would be also searching the literature for rotameric
> preferences and figuring out the applied dihedral potential that,
> applied over top of your explicit solvent simulation, would give you
> the correct distribution of dihedral angles.
> As for your mdp file for step 2, I'd think that you want it to be
> exactly as you will eventually use for simulation with respect to the
> Let me note once again that this is just what comes to my mind. I
> haven't done it and ff development is just about the most difficult
> topic in our field.
> -- original message --
> Dear Gromacs developer:
> I am asking for your help about fitting a dihedral angle parameters using
> gromacs md simulation. One article (link:
> http://www.mpip-mainz.mpg.de/~andrienk/journal_club/opls.pdf) says that
> fitting a dihedral angle potential parameters needs three steps: 1)
> perform ab initio calculation; 2) do md simulation by setting the dihedral
> angle parameters to zero; 3) fit all the parameters by comparing the md
> energies and ab initio energies.
> I am now working on a dihedral angle fitting and I have done step 1. But I
> don't know how to do step 2 and 3. For example, if I want to fit a
> CT-CT-CT-CT dihedral angle for butane, how do I prepare for my *.mdp file,
> and after md simulation, how to fit the md energies to the ab initio
> Would you please help me?
> Thank you.
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