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 vedat > >>>> 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 -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
