[gmx-users] Tabulated potentials make newbies crazy

ms devicerandom at gmail.com
Mon Nov 30 13:38:04 CET 2009

Mark Abraham ha scritto:
 > Sorry, I was a bit incomplete last night. Charge groups are the
> fundamental unit for neighbour-searching (3.4.2) to construct lists of
> charge groups for nonbonded interactions, which determine lists of
> atom-atom interactions. However, the nonbonded interactions are
> evaluated as nested sums, first over energy groups. So for energy groups
> of Protein and SOL, the neighbour search finds all pairs of charge
> groups that are both Protein and inside the cutoffs, and lists them.
> Then all Protein-SOL similarly, then all SOL-SOL. This requires that the
> energy groups be a union of only complete charge groups (and I am not
> aware that this is spelled out anywhere in the manual!). So for energy
> groups of Calpha, Rest_of_Protein and SOL, it would be necessary to use
> an individual charge group for each Calpha. This would usually mean it
> has a net non-integral charge that is equal in magnitude of the charge
> of the group from which it is taken. It is well known that small charge
> groups of non-integral charge can then wander back and forth across
> cut-off boundaries and generate artefacts.

Ok, thanks for the clarification. This doesn't suggest a trivial
solution to the problem, quite the opposite: I understood correctly that
charge groups must be neutral, and this is impossible to do if we put
each C-alpha as a charge group.

I can coarse the thing further -that's quite the plan, actually- and
eliminate electrostatics, but I hoped to have a look at what happens
with the new potential and getting it right, before going so far.

So, even if the following:
>> The problem is that since I have a single molecule now, and the single
>> molecule must be neutral, so it must be all a single charge group
>> ("Therefore we have to keep groups of atoms with total charge 0
>> together. These groups are called charge groups.", 4.6.2).

is not entirely correct, it is indeed correct that charge groups
*should* be neutral. Isn't it?

> If you're running in single precision, that precision cannot represent
> values as large as 10^41. Since in any simulation (but particularly
> coarse-grained one) non-bonded atoms aren't going to get this close, the
> values are next to irrelevant. Just choose 10^38 for anything larger
> than that.

Right, it is probably precision problem. Thanks.

>>>> Now, my questions are:
>>>> - What is the accepted range of values in tables?
>>> I don't think this is the problem.
>> It is the least problem probably, given my confusion on energy-charge
>> groups, but it seems it is too...
>>>> - How do I define a steep repulsion potential correctly?
>>> It's terse, but manual 6.7 seems to have the necessary information.
>> 6.7 is one of the references I am obviously using, but it gives only
>> general (even if essential!!) information, nothing speficic on "good" or
>> "bad" potential shapes/values. But probably that's the least problem :)
> Knowing a sensible shape is your problem, if you're choosing to
> unbalance the force field by changing one of the contributing potentials...

I meant "sensible" in the meaning of "can be interpolated more or less
faithfully / will be calculated with more or less artefacts" -of course
if it makes sense in the model is my problem...

> Best of luck!

It seems to be in scarce supply these days (just lost a fellowship, argh).


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