Thanks for the clarification, that explains everything. Perhaps page 112 of the v4 manual could be updated too :
"generate pairs = no (the default, get 1-4 interactions from the pair list, when parameters are not present in the list give a warning and use zeros) or yes (generate 1-4 interactions which are not present in the pair list from normal Lennard-Jones parameters using FudgeLJ)" Replacing 'interactions' with 'parameters' would make things clearer here too.. Regards Mike On Tue, Jul 14, 2009 at 12:55 PM, Berk Hess<[email protected]> wrote: > Hi, > > Again, to avoid confusion: > there are two (or three) completely separate parts to this issue in Gromacs. > > 1) The generation of the actual pair interactions in the [ pairs ] section > in the topology (.top) file. pdb2gmx does this for you. > If you write a topology by hand, you also have to add the 1-4 interactions > in the [ pairs ] section by hand. > > 2) The generation of the interaction parameters for the interactions > in the [ pairs ] section. This is what gen-pairs switches and this is what > the comment in the manual is about. Pair parameters are taken from > the [ pairtypes ] section in the force field file or topology file. > If parameters are not found for a certain pair of atom types in [ pairtypes > ], > they will be generated when gen-pairs is true, a fatal error will be > generated when gen-pairs is false. > (I will change "interactions" to "interaction parameters" in the quoted > line of the manual.) > > 3) pairs are bonded interactions and bonded interactions in no way affect > the calculation of non-bonded interactions in Gromacs. Thus to not calculate > interactions twice, you need to use nrexcl=3 when you put 1-4 interactions > in the [ pairs ] section. > > Berk > > ________________________________ > Date: Tue, 14 Jul 2009 13:43:19 +0300 > From: [email protected] > To: [email protected] > Subject: Re: [gmx-users] Re: Problems with non-bonded interactions using > OPLSAA > > Hi. > I found the same behavior with both 3 (3.3.3) and 4 (4.0.5) versions on > x86_64. > What I found is : > 1. gen-pair correctly generates the 1-4 parameters (verified with gmxdump -s > topol.tpr) > But with no [pairs] defined, 1-4 interactions > are not calculated no matter what the scale factor is. > One has to define the [pairs] to calculate scaled 1-4. > 2. It seems that in the case of nrexcl 2 and pairs defined, the 1-4 > interactions are calculated twice > (once with scaling 1 in LJ(SR) and once scaled by whatever the scaling > factor is in LJ-14) > With nrexcl 3 and pairs defined only the scaled 1-4 are calculated. > > Probably the manual is not clear at this point (p.99 of v4 manual), where it > states : > The GROMOS force fields list all these interactions explicitly, but this > section might be > empty for force fields like OPLS that calculate the 1-4 interactions by > scaling. > > To verify this I did : > zero steps with a single molecule in a large box, varying nrexcl and scaling > factors with pairs defined. > What I found is : > NREXCL SCALE FACTOR LJ(SR) LJ-14 > 2 0.0 3.22186 > 0 > 2 0.5 3.22186 > 2.58086 > 2 1.0 3.22186 > 5.16172 > 3 0.0 -1.93987 > 0 > 3 0.5 -1.93987 > 2.58086 > 3 1.0 -1.93987 > 5.16172 > > Scaling in 1-4 works as it is expected. > The total LJ (LJ(SR) + LJ-14) in the case of nrexcl 3 and scale factor 1.0 > is 3.22185 that is equal to > the LJ(SR) in the case of nrexcl 2 and scale factor 0. This means that with > nrexcl 2, > the 1-4 are calculated unscaled no matter the value of scaling factor AND > scaled by scaling factors, > i.e. scaling 1.5 instead of 0.5 as Mike notes, > Similar for Coulombic interactions. > What I use is nrexcl 3 and pairs defined. > > DD > > > > > Berk Hess wrote: > > Hi, > > There is surely no problem with the gen-pairs option, as that would cause > serious trouble with nearly all simulations performed with Gromacs. > > gen-pairs only sets the generation of pair parameters, not of the actual > pair interactions in the topology. > > I have no clue to what it going wrong in your system. > You can file a bugzilla at bugzilla.gromacs.org. > > Berk > >> Date: Mon, 13 Jul 2009 21:09:37 +0200 >> From: [email protected] >> To: [email protected] >> Subject: [gmx-users] Re: Problems with non-bonded interactions using >> OPLSAA >> >> Dear all >> >> I have since found the problem. For some reason gen-pairs = yes option >> is not working, so my 1-4 interactions were being completely excluded >> and not scaled by 0.5 as they should have been. Defining all 1-4 pairs >> in a [ pairs ] section in conjunction with nexcl =3 in the topology >> solved the problem. >> >> I was not sure whether to use nexcl =2 or nexcl =3 in the case of >> scaled 1-4 interactions, but by trial and error I found that one >> should use nexcl =3, otherwise you have the full 1-4 interaction + the >> scaled one, so in total a scaling of 1.5 instead of 0.5. >> >> Any ideas why gen-pairs = yes option is not working would be much >> appreciated. >> >> Thanks to those who responded to my first email, >> >> Mike >> >> >> >> On Thu, Jul 2, 2009 at 6:54 PM, Mike Wykes<[email protected]> wrote: >> > Dear all >> > >> > I would like to simulate beta cyclodextrin in various organic >> > solvents with the OPLSAA FF for Carbohydrates (J Comput Chem 18: >> > 1955-1970, 1997) but am having problems with the short range Coulomb >> > and LJ interactions. >> > This FF (and OPLS in general) does not assign LJ parameters to >> > hydrogen atoms in OH groups, relying on the repulsion between oxygens >> > to keep the hydrogen (charge +0.435 ) of one OH group getting too >> > close to the O (charge -0.7 ) of another. >> > However in MD simulations, the hydrogen of one OH group collides with >> > the O of another, and shortly after the system explodes. >> > >> > Obviously, this could be a mistake of how I converted the parameters >> > in the paper into gromacs parameters, so I have checked this and found >> > no mistakes. Some of the parameters are taken from regular OPLS, >> > allowing me to check my conversion by comparing to the parameters in >> > gromacs/share/top/ffoplsaa*.itp files. >> > >> > Out of curiosity I implemented the same forcefield in the tinker md >> > package and the O...H system was stable during MD, with no O..H >> > collisions. Comparing the energies of exactly the same geometry of >> > beta cyclodextrin with the same OPLS parameters shows identical bonded >> > interactions, but differences in the non-bonded interactions: >> > >> > tinker(kcal/mol) gmx (kj/mol) gmx(kcal/mol) >> > difference >> > Total Potential energy 312 -1416.98 -338.67 650.67 >> > Bond Stretching 23.32 97.58 23.32 0 >> > Angle Bending 30.38 127.11 30.38 0 >> > Torsional Angle 312.06 1305.64 312.06 0 >> > Van der Waals 13.69 -119.03 -28.45 42.14 >> > Charge-Charge -67.45 -2828.29 -675.98 608.52 >> > >> > In both cases the molecule was in the gas phase, all non-bonded >> > interactions being treated with a cutoff of 1.5 nm. >> > >> > Any suggestions as to what could be going wrong in my gromacs >> > calculations would be much appreciated. >> > >> > Please find my mdp, top and itp files below. I am using version 4.0.5. >> > >> > Many thanks, >> > >> > Mike >> > >> > >> _______________________________________________ >> 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 > > ________________________________ > Express yourself instantly with MSN Messenger! MSN Messenger > > ________________________________ > _______________________________________________ > 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 > > ________________________________ > Express yourself instantly with MSN Messenger! MSN Messenger > _______________________________________________ > 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 > _______________________________________________ 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
