[gmx-users] Re: decoupling charge while maintaining intramolecular potentials

Berk Hess gmx3 at hotmail.com
Wed Jan 28 10:57:09 CET 2009


I guess that what you want to do is exactly what the decouple mdp options do.
You probably don't need modify any topology files.
If couple-intramol=no (default) than all intra-molecular interactions are not turned
off and are plain LJ/Coulomb without cut-off.


> Date: Wed, 28 Jan 2009 00:07:43 -0500
> From: chris.neale at utoronto.ca
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Re: decoupling charge while maintaining intramolecular	potentials
> Thank you Michael for the detailed reply, I have posted clarifications  
> and additional questions or remarks inline below.
> > Hi, Chris-
> >
> > I unfortunately can't be too much help, because my free energy
> > calculations are done through a modified version of Gromacs 3.1.4, and
> > I am currently working with Berk and Erik to get the important
> > modifications into the 4.0 branch.
> >
> >> I am a new user of the free energy code. I am somewhat confused
> >> regarding the method that should be applied to decouple the long range
> >> interactions of the solvent from the solute while still maintaining
> >> intramolecular long-range interactions for the solute.
> >
> > By long range interactions, you mean the ones outside the cutoff,
> > correct?  Because there's another set of difficulties dealing with the
> > ones that are shortange nonbonded interactions as well.  Could you
> > clarify?
> When I said "long-range" I should have said "non-bonded" instead  
> throughout this entire document. Sorry for the incorrect terminology.  
> Therefore I am under the impression that one wants to decouple the  
> intermolecular solvent-solute nonbonded interactions without affecting  
> any intramolecular nonbonded interactions. I have seen this applied in  
> your papers and some others, many of them done via charmm.
> >
> >> I was able to find some information in this thread:
> >> http://www.gromacs.org/pipermail/gmx-developers/2006-January/001498.html
> >> but it is still unclear to me.
> >
> > I'm not surprised, it was unclear for us at the time as well :)
> >
> >> I have reproduced the methane and tip3p energies of solvation based on
> >> the tutorial that is on the gromacs wiki. In this case, I simply
> >> assigned new charge values of 0 in the B state without making any
> >> special considerations for intramolecular O-H values. However, tip3p
> >> is rigid and perhaps maintaining the intramolecular q-q and LJ
> >> components is not essential in this case.
> >
> > This is where I get confused -- are you talking about long range, or
> > any intramolecule interactions.  Certainly for methane and tip3p,
> > there aren't any, because all atoms are 1,3 neighbors.
> I am talking about any nonbonded intramolecular interactions. Further,  
> your point regarding 1-2 and 1-3 interactions is well taken. My  
> molecule of interest is a dodecylphosphocholine detergent and  
> therefore there will be substantial intramolecular nonbonded  
> interactions that I believe it would be best to maintain.
> >
> >> 1. Is it necessary to maintain the intramolecular long-range
> >> interactions for the solute while decoupling LJ or charge? If not
> >> absolutely required, does it affect the rate of convergence?
> >
> > If you change the intramolecular nonbonded interactions, then you
> > would have to perform a second vacuum calculation in which you turn
> > them back on.   In terms of rates of convergence -- nobody really
> > knows.  If it's a intramolecular hydrogen bonding system, then turning
> > off the intramolecular interactions might be faster.
> What I am actually doing is annihilating one DPC detergent from a DPC  
> micelle and, separately, annihilating one DPC detergent monomer from  
> bulk water. The dG(monomer) minus dG(micelle) should then be related  
> to the relative probabilities of monomeric and aggregated states. I  
> have left out the monomer restraints and the volume correction here  
> for simpicity. It is my impression that this monomer-in-bulk  
> annihilation provides the second simulation that you mentioned above,  
> although I will still require this second simulation even if I  
> maintain my intramolecular non-bonded interactions since I am  
> interested in the relative probabilities of the monomeric and  
> aggregated state, both in solution, and not in solvation free energies.
> The reason that I thought one would want to not change the  
> intramolecular interactions is that it seems to me that this will make  
> the d(pot)d(lambda) energies larger and then subtracting 200-190=10  
> seems like it will have more uncertainty than if the dvdl integrated  
> energies were all smaller. This is just based on the idea that a small  
> difference of two large numbers is often difficult to obtain precisely.
> However, I see your point about relatively stable intramolecular  
> interactions. I will need to think further about that one.
> >
> >> 2. Is this already handled by the free-energy code?
> >
> > I can't speak for the 4.0 code.  Berk was introducing nonbonded pair
> > terms such that these pair terms would overrule the 'alchemical'
> > transformation, resulting in unchanged intramolelcular nonbonded
> > interactions.  I actually don't know the current state of this change,
> > though.
> >
> >> 3. If not, how might one go about doing this? My confusion with some
> >> additional [ pairs ] entry is how gromacs would get the right
> >> combination for lambda=0 and lambda=1 (not to mention intermediate
> >> states).
> >
> > I'm a bit confused.  I would think that you would just want to set
> > them to the lambda=0 state, so that intramolecular interactions were
> > preserved.  Am I thinking of something different than you are?
> If you're just talking about how to handle the lambda=1 simulation by  
> setting pairs according to the nonbonded values that are achieved in  
> the lambda=0 state, then I believe that we are thinking about the same  
> thing. However, it gets messy for intermediate values of lambda (not  
> to mention impossible for the charging simulations) so I'll outline my  
> logic more elaborately below.
> Assume that the 4.0.3 free-energy code uses lambda to scale all  
> nonbonded interactions including intreamolecular ones for the  
> annihilated molecule. Further assume that I create a new [ pairs ]  
> section that entirely accounts for all intramolecular LJ interactions  
> of the DPC to be annihilated (let's talk LJ annihilation only to make  
> this part simpler). If I include this new pairs section for lambda=1,  
> then I expect no solute-solvent nonbonded interactions but to maintain  
> regular intramolecular nonbonded interactions from the pairs section.  
> However, if I include this new pairs section for lambda=0.5, then I  
> expect to have 1.5x strength nonbonded intramolecular interactions for  
> the annihilated solute (once from pairs and one-half from regular  
> nonbonded). This would require different .itp files for each lambda  
> value with pairs set according to:
> pair(lambda)=pair(Astate)*(1-lambda) + pair(Bstate)*(lambda)
> if the conversion from A state to B state is linear and thus the new  
> pairs section would be different for each lambda and would compensate  
> for the loss of intramolecular nonbonded interactions as lambda is  
> increased.
> Still, I believe that it is not yet possible to define coulombic  
> interactions in the pairs section so this would not work for the  
> coulombic portion.
> Thanks you,
> I sincerely appreciate your time in assisting me,
> Chris.
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