[gmx-developers] scaling 1-4 electrostatic interactions
chris.neale at utoronto.ca
chris.neale at utoronto.ca
Sun Mar 9 17:33:47 CET 2008
Quoting hessb at mpip-mainz.mpg.de:
>> Quoting David van der Spoel <spoel at xray.bmc.uu.se>:
>>> chris.neale at utoronto.ca wrote:
>>>> I am wondering why there is a [ pairtypes ] section only for LJ and
>>>> not coulombic. I have been able to trick gromacs into properly
>>>> combining two forcefields that have a different fudgeQQ, but that
>>>> trick is fairly specific:
>>> Without looking things up you could use multiple pair interactions for
>>> each pair, but that will only help if one fudgeQQ_A = n * fudgeQQ_B
>>> with n integer.
>> Thank you for your comments. This is exactly what I have done. Where
>> fudgeQQ_A = 0.5 (opls) and fudgeQQ_B = 1.0 (lipids). I then specify [
>> pairtypes ] for group B as half of what they should be and include the
>> 1-4 pairs twice for group B, while setting fudgeQQ = 0.5. At first
>> glance it is simple enough to warrant only a single sentence in a
>> methods section, but I had to test it since one can imagine that a
>> second pair might overwrite the first or something else unexpected
>> since I don't think that gromacs was coded with this usage in mind. In
>> fact it works perfectly with the only difference being rounding errors
>> from slightly different mathematical form (two calculations instead of
>>>> I am in the process of writing up the results of my protein-lipid
>>>> simulations and I am currently trying to decide how to split the
>>>> paper. I would like to split the method plus proof-of-concept
>>>> section out into a simple one page methods letter but in that case
>>>> I would need to convince the reader that the method that I have
>>>> used is necessary and could not easily be replaced by a slight code
>>>> modification to gromacs. In fact this may be the case and is the
>>>> reason why I am writing to this list.
>>>> First: is there some important reason why a [ coulombic-pairtypes ]
>>>> section could not exist, or is it just that nobody has dedicated a
>>>> day of coding to make this happen? I figure that PME could make it
>>>> more difficult, but don't really know.
>>>> Second: is gromacs 4.x likely to allow users to arbitrarily set
>>>> coulombic 1-4 interactions in the same way that this can be done
>>>> for LJ 1-4 interactions by [ pairtypes ] ?
>>> Section VIII of the gromacs 4 paper desribes very briefly the new
>>> tabulated bonded potentials. It could however be that there is not
>>> something like a Coulomb interaction, that multiplies a function by the
>>> charges (like there is for non-bonded potentials). Maybe Berk can
>> Thanks for pointing this out. I did take a look at this section, but
>> didn't find any particular mention here for exactly what I am
>> describing. For other readers, the section referred to reads:
>> "User defined nonbonded interactions that can be assigned
>> independently for each pair of charge groups were already supported,
>> and we have now additionally implemented user defined bonds, angles,
>> and dihedrals functions."
>> It would be great if you could comment here Berk.
>> Thank you again,
> User defined bond potentials can do what you want.
> But it might be very tedious, depending on the complexity of your system.
> Everything is described in the CVS pdf manual.
> You have c*f(r) at your disposal, where one could choose
> c and f different for every atom pair you defined.
> So you could set fudgeQQ to zero and define all Coulomb-14 through tables.
> But if you need many different atom pairs with different charges,
> you need to define the proper c for every one.
> But it would be much better to be able to set fudgeQQ per molecule,
> which by itself would not be difficult, but we would need to
> extend the top file format.
Thank you for the explanation. Are you likely to include the
per-molecule fudgeQQ in gromacs 4.x? I think that it would be a good
thing to include but am mostly just interested in knowing if you are
likely to include it.
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