[gmx-users] mix berger ff with opls

BIN ZHANG zhngbn at gmail.com
Sun Mar 14 20:55:05 CET 2010

Dear Chris:

Thanks a lot for your reply. That's really helpful. Now I have a  
further question:
> "1,4 electrostatic inter-actions were reduced a factor of 2 and 1,4  
> Lennard?Jones interactions a factor of 8."

I can understand that the LJ1-4 can be reduced by simply scale epsilon  
in [pairtypes], how about 1,4 electrostatics? Since fudgeQQ is 1, how  
is the factor of 2 achieved?


p.s. your paper looks really good, congrats!

> Note that the 0.125 scaling factor is not anything that you need to  
> do in addition to the files that you can download from Tieleman's  
> site -- it is already included there (you can confirm this for  
> yourself by looking at the topologies downloaded form there). This  
> is because the 0.125 scaling (1/8 scaling) of 1-4 LJ is part of the  
> original Berger lipids.
> Note that the "Berger" lipids were in fact developed by many people  
> and they have come to be named by only one of the contributors. The  
> reference that I use for my 1/8 scaling of the LJ 1-4 is:
> Lindahl, E., and O. Edholm. 2000. Mesoscopic undulations and  
> thickness fluctuations in lipid bilayers from molecular dynamics  
> simulations. Biophys. J. 79:426?433.
> where they state in the methods:
> "1,4 electrostatic inter-actions were reduced a factor of 2 and 1,4  
> Lennard?Jones interactions a factor of 8."
> I believe that this idea originated in a Jorgensen paper looking at  
> bulk simulations of n-alkanes, but ashamedly I can't recall for sure  
> at this moment. If you need it, I can look it up next week (let me  
> know).
> BTW, the half-epsilon double-pairlist method is finally published.  
> The reference is Biophys J. 2010 Mar 3;98(5):784-792. "An Iris-Like  
> Mechanism of Pore Dilation in the CorA Magnesium Transport System."  
> Chakrabarti N, Neale C, Payandeh J, Pai EF, Pomès R.
> In our paper, I attempt to give a more complete description of the  
> development of this lipid forcefield by writing:
> The parameters for DMPC lipids (10) were the united atom  
> representation first proposed by Egberts et al. (18), with charges  
> from Chiu et al. (19) adjusted by Berger et al. (20), and with the  
> additional scaling of 1-4 coulombic terms introduced by Lindahl and  
> Edholm (21).
> My description of the HEDP method in the referenced paper is thus:
> We mixed the OPLS-AA protein force field with the Berger lipid  
> parameters consistently by applying the half-epsilon double-pairlist  
> method introduced in this work. This method avoids  
> reparameterization (22) and retains the original parameters with  
> greater fidelity. Specifically, the epsilon-values of the 1-4  
> Lennard-Jones (LJ) parameters of the lipids are divided by two in  
> the pair types section of the GROMACS input file, and the list of  
> 1-4 interactions is duplicated in the topology file of each lipid.  
> The regular OPLS combination rules are then applied. In this way,  
> the lipidic LJ and Coulombic 1-4 parameters are both cut in half and  
> then included twice to yield properly scaled 1-4 interactions for  
> both lipids and OPLS protein.
> Hope this helps,
> please post again to the list if you have further question.
> Chris.
> -- original message --
> Dear all:
> I was trying to convert the lipid.itp downloaded from Tieleman's
> website to the format compatible with OPLS. I basically followed the
> procedure in this post, which is really helpful:
> http://www.mail-archive.com/gmx-users@gromacs.org/msg03459.html
> But there is one comment there I don't understand:
> after changing c6/c12
> to sigma/epsilon. (gives effective fudgeLJ of 0.125).
>  Can someone please explain what this means? Why do I have this
> effective fudgeLJ?
> Thanks a lot,Bin
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