[gmx-users] suitable parameter settings for intermolecular non-bonded interaction

vedat durmaz durmaz at zib.de
Wed Mar 31 18:44:10 CEST 2010

Mark Abraham schrieb:
> On 31/03/2010 11:44 PM, vedat durmaz wrote:
>> thanks to both of you for your helpful hints. actually, i'm not using
>> the LIE method as available with the gromacs package, but planning to
>> implement the model myself using energies from gromacs runs.
> Sure... it's still only an algorithm that generates a fairly coarse
> approximation.

actually, any result gained by simulations is an approximation in some
way. anyways, is there a much more reliable method for predicting
binding affinities that you would eagerly like to recommend? feel free
to tell me if so!
>> be that as it may, one thing remained unclear (see below please).
>>   Mark Abraham schrieb:
>>> On 31/03/2010 9:15 PM, vedat durmaz wrote:
>>>> hello out there,
>>>> i'm trying to simulate a receptor ligand system in order to extract
>>>> intermolecular non-bonded interaction energies (vdw/coulomb) and apply
>>>> the linear interaction energy model.
>>> Agreed on Sander's point, here.
>>>> which parameter settings do you recommend for highly accurate results?
>>>> up to now, i had chosen (copied from somewhere :)
>>> Well, write it down, because you'll need to defend your choices
>>> later :-)
>>>> rlist                = 1.2
>>>> vdwtype              = shift
>>>> rvdw                 = 1.0
>>>> rvdw-switch          = 0.9
>>>> coulombtype          = PME-Switch ; PME
>>>> rcoulomb             = 1.1
>>>> resulting in LJ-14 = 0, and Coulomb-14 = 0 (which i "intuitionally"
>>>> prefer to LJ-SR and Coulomb-SR).
>>> I've no idea what you mean by this.
>> what i mean is that after having applied "g_energy" to the energy output
>> file in order to extract non-bonded energies, all "Coulomb-14" and
>> "LJ-14" terms shape up to be equal to zero (as if they haven't been
>> calculated),
> Well that means they weren't calculated. Whether that's reasonable
> depends on your forcefield.
>>  but "Coulomb-SR" and "LJ-SR" are plausible decimal numbers
>> like for example -48.1234. though, at the moment i "tend" to operate on
>> *-14 energies. how can i tell gromacs to compute these terms?
> *Tend*? Your usage of that word makes no scientific sense that I can
> see. What on earth is more significant about non-bonded interactions
> between atoms separated by 3 bonds than other non-bonded interactions?
> :-)
> Mark

i see. that was a misunderstanding on my part. i thought (had read
somewhere) that the *-14 interaction would include both *-SR and *-LR
(short range and long range) interaction. if the *-SR energies are
suitable for the LIE method, i'll be the happiest guy in the world. just
need to find some proper cut-offs.

thanks again


>>>> i have a box of 8.1857 x 8.1857 x 8.1857 nm. Is it helpful to increase
>>>> rcoulomb and rvdw up to e.g. 8.0 and rvdw-switch up to 4.0 or/and
>>>> should
>>>> i take vdwtype=cut-off instead of shift?? what's the difference?
>>>> how can
>>>> i get my LJ-14/Coulomb-14 terms? can anyone provide a well-working
>>>> combination of parameter settings for non-bonded interactions within a
>>>> system as described above?
>>> As I wrote earlier today, haphazardly varying parameters is not what
>>> you want to do. Merely increasing these cut-offs may feel like "more
>>> accuracy", but computing a more expensive approximation to a
>>> theoretical model is not necessarily any good, because the parameters
>>> you are using were developed for some different cut-off. It does not
>>> follow that the parameters are transferable to other contexts. You
>>> should aim to use a model physics for which the parameters were
>>> developed, or for which they were subsequently proved to be effective.
>>>> that's quite a lot questions, i know.
>>>> gromacs says: "Refer to the primary literature for your of choice for
>>>> the recommended settings". However, i couldn't find any
>>>> recommondations
>>>> for ffamber99 (ffamber99sb is what i use) in the pdf documents
>>>> provided
>>>> with the amber port's download.
>>> They're not primary literature. Refereed publications tend to
>>> accompany the introduction of forcefields, and they are mandatory
>>> reading. AMBER (port)'s webpage will tell you what to read. Also
>>> search for subsequent work by the same authors, for they are probably
>>> using best practice for their own forcefield...
>>> Mark

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