Hi Dorota, please keep all such correspondence on the gromacs mailing
list. One can then send somebody a personal email indicating that you
would appreciate it if they took a look. I have copied this answer to
the list. Please respond there.
Quoting Dorota Jamróz <[email protected]>:
Hallo Chris,
While searching for information about a possibility to combine the Berger
lipid FF with the OPLSA-AA I came across your posts at the gmx-users forum
and also your text on the subject you made available on the net.
I am a GROMACS beginner and I haven't yet mastered all the nuances of the
program, which may be the reason of my problem, but I must admit I cannot
understand the philosophy of your method. I would be very grateful if you
could answer my questions and clear my doubts.
To begin with - I presume, the main idea of the procedure is to modify the
non-bonded parameters from the Berger FF so that the potential energy for
the lipid, as calculated with the OPLS-AA formulas, gives the proper value
(i.e same as it would be if calculated with Berger FF). Am I right on this
point?
Yes, as calculated with the OPLS-AA *1-4 rules*
Next - I understand the main problem is the scaling of the 1-4 potential,
which is 1 for Berger (i.e no scaling) and 0.5 for OPLS-AA (i.e. only half
of the 1-4 potential is included into the total potential).
If it is so then I would say, in order to get the proper 1-4 LJ potential
you should either MULTIPLY the Berger epsilons by 2 or leave them as they
are but insert a second copy of [ pairs ] into your topology file. Your
solution was to DIVIDE the Berger epsilons by 2 AND include two [ pairs ]
section. With the FudgeLJ = 0.5, as defined by OPLS-AA, the calculated LJ
1-4 potential will be then half of the proper value (taking half of the
1-4 LJ potential calculated with epsilons divided by 2 gives you 0.25 of
the proper value. You sum these interaction twice, so finally you get the
V(OPLS)=0.5V(Berger) )
The method is sound. A key realization is that the [ pairs ] section
defines both the LJ and the Q pairs, so we will have double of each.
We actually want double Q, since it was cut to 0.5 and 0.5*2=1.0. What
we don't actually want is double epsilon, since the epsilon in
question is already a special pairtypes epsilon that has been properly
modified for 1-4 interactions. We thus cut epsilon in half to
counteract the fact that we are forced to add it again twice in the
pairs section.
But don't take my word for it. Do a zero-step mdrun and look at your
energy breakdown via g_energy for both lipid.itp/ffgmx and the hedp
method. This is one of the things that I did to ensure that not only
the idea was sound but there were not any unexpected bugs that would
come to the surface with a double pairs list.
Another point concerns the 1-4 Coulombic interaction; you state that
dividing the Berger epsilons by 2 will modify both the 1-4 interactions
types, the LJ and the Coulombic ones.
I don't believe that I do say that anywhere.
In what way will the Coulombic
potential be changed? It does not depend on the epsilon value and, as I
understand, there is no way to define another subset of charges for the
1-4 Coulomb interaction. The only way GROMACS allows you to modify this
potential for specified pairs of atoms is to include it twice in the total
potential, if a given pair is found in the [ pairs ] section.
Summarizing, it seems to me that the 1-4 potential calculated with the
parameters changed according to your method will give the right Coulombic
potential but only half of the proper LJ potential.
While I am always open to the possibility that I have made a mistake,
I actually put a lot of time into developing this and distributing it,
so I'm not very motivated to go look into it again before I see a bit
of data or perhaps a proper mathematical derivation of whatever
problem you propose. I still believe that the method is properly
derived and implemented.
Chris.
As I wrote, it's pretty possible I am a victim to some misconception about
how GROMACS works. In any case I would very grateful for you comment.
Cheers,
Dorota
--
Dorota Jamróz, Ph.D
Faculty of Chemistry
Jagiellonian University
ul.Ingardena 3, 30-060 Cracow, POLAND
Phone: (+48) 012 6632263
e-mail: [email protected]
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