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Hi,<br><br>I changed that part as well and also updated it for the fact that grompp<br>in 4.0 never generates zero parameters, but always generates a fatal error<br>when parameters are missing.<br><br>Berk<br><br>> Date: Tue, 14 Jul 2009 14:21:49 +0200<br>> Subject: Re: [gmx-users] Re: Problems with non-bonded interactions using OPLSAA<br>> From: mikewykes@gmail.com<br>> To: gmx-users@gromacs.org<br>> <br>> Thanks for the clarification, that explains everything.<br>> <br>> Perhaps page 112 of the v4 manual could be updated too :<br>> <br>> "generate pairs = no (the default, get 1-4 interactions from the pair<br>> list, when parameters are<br>> not present in the list give a warning and use zeros) or yes (generate<br>> 1-4 interactions which<br>> are not present in the pair list from normal Lennard-Jones parameters<br>> using FudgeLJ)"<br>> <br>> Replacing 'interactions' with 'parameters' would make things clearer here too..<br>> <br>> Regards<br>> <br>> Mike<br>> <br>> On Tue, Jul 14, 2009 at 12:55 PM, Berk Hess<gmx3@hotmail.com> wrote:<br>> > Hi,<br>> ><br>> > Again, to avoid confusion:<br>> > there are two (or three) completely separate parts to this issue in Gromacs.<br>> ><br>> > 1) The generation of the actual pair interactions in the [ pairs ] section<br>> > in the topology (.top) file. pdb2gmx does this for you.<br>> > If you write a topology by hand, you also have to add the 1-4 interactions<br>> > in the [ pairs ] section by hand.<br>> ><br>> > 2) The generation of the interaction parameters for the interactions<br>> > in the [ pairs ] section. This is what gen-pairs switches and this is what<br>> > the comment in the manual is about. Pair parameters are taken from<br>> > the [ pairtypes ] section in the force field file or topology file.<br>> > If parameters are not found for a certain pair of atom types in [ pairtypes<br>> > ],<br>> > they will be generated when gen-pairs is true, a fatal error will be<br>> > generated when gen-pairs is false.<br>> > (I will change "interactions" to "interaction parameters" in the quoted<br>> > line of the manual.)<br>> ><br>> > 3) pairs are bonded interactions and bonded interactions in no way affect<br>> > the calculation of non-bonded interactions in Gromacs. Thus to not calculate<br>> > interactions twice, you need to use nrexcl=3 when you put 1-4 interactions<br>> > in the [ pairs ] section.<br>> ><br>> > Berk<br>> ><br>> > ________________________________<br>> > Date: Tue, 14 Jul 2009 13:43:19 +0300<br>> > From: ntelll@gmail.com<br>> > To: gmx-users@gromacs.org<br>> > Subject: Re: [gmx-users] Re: Problems with non-bonded interactions using<br>> > OPLSAA<br>> ><br>> > Hi.<br>> > I found the same behavior with both 3 (3.3.3) and 4 (4.0.5) versions on<br>> > x86_64.<br>> > What I found is :<br>> > 1. gen-pair correctly generates the 1-4 parameters (verified with gmxdump -s<br>> > topol.tpr)<br>> > But with no [pairs] defined, 1-4 interactions<br>> > are not calculated no matter what the scale factor is.<br>> > One has to define the [pairs] to calculate scaled 1-4.<br>> > 2. It seems that in the case of nrexcl 2 and pairs defined, the 1-4<br>> > interactions are calculated twice<br>> > (once with scaling 1 in LJ(SR) and once scaled by whatever the scaling<br>> > factor is in LJ-14)<br>> > With nrexcl 3 and pairs defined only the scaled 1-4 are calculated.<br>> ><br>> > Probably the manual is not clear at this point (p.99 of v4 manual), where it<br>> > states :<br>> > The GROMOS force fields list all these interactions explicitly, but this<br>> > section might be<br>> > empty for force fields like OPLS that calculate the 1-4 interactions by<br>> > scaling.<br>> ><br>> > To verify this I did :<br>> > zero steps with a single molecule in a large box, varying nrexcl and scaling<br>> > factors with pairs defined.<br>> > What I found is :<br>> > NREXCL SCALE FACTOR LJ(SR) LJ-14<br>> > 2 0.0 3.22186<br>> > 0<br>> > 2 0.5 3.22186<br>> > 2.58086<br>> > 2 1.0 3.22186<br>> > 5.16172<br>> > 3 0.0 -1.93987<br>> > 0<br>> > 3 0.5 -1.93987<br>> > 2.58086<br>> > 3 1.0 -1.93987<br>> > 5.16172<br>> ><br>> > Scaling in 1-4 works as it is expected.<br>> > The total LJ (LJ(SR) + LJ-14) in the case of nrexcl 3 and scale factor 1.0<br>> > is 3.22185 that is equal to<br>> > the LJ(SR) in the case of nrexcl 2 and scale factor 0. This means that with<br>> > nrexcl 2,<br>> > the 1-4 are calculated unscaled no matter the value of scaling factor AND<br>> > scaled by scaling factors,<br>> > i.e. scaling 1.5 instead of 0.5 as Mike notes,<br>> > Similar for Coulombic interactions.<br>> > What I use is nrexcl 3 and pairs defined.<br>> ><br>> > DD<br>> ><br>> ><br>> ><br>> ><br>> > Berk Hess wrote:<br>> ><br>> > Hi,<br>> ><br>> > There is surely no problem with the gen-pairs option, as that would cause<br>> > serious trouble with nearly all simulations performed with Gromacs.<br>> ><br>> > gen-pairs only sets the generation of pair parameters, not of the actual<br>> > pair interactions in the topology.<br>> ><br>> > I have no clue to what it going wrong in your system.<br>> > You can file a bugzilla at bugzilla.gromacs.org.<br>> ><br>> > Berk<br>> ><br>> >> Date: Mon, 13 Jul 2009 21:09:37 +0200<br>> >> From: mikewykes@gmail.com<br>> >> To: gmx-users@gromacs.org<br>> >> Subject: [gmx-users] Re: Problems with non-bonded interactions using<br>> >> OPLSAA<br>> >><br>> >> Dear all<br>> >><br>> >> I have since found the problem. For some reason gen-pairs = yes option<br>> >> is not working, so my 1-4 interactions were being completely excluded<br>> >> and not scaled by 0.5 as they should have been. Defining all 1-4 pairs<br>> >> in a [ pairs ] section in conjunction with nexcl =3 in the topology<br>> >> solved the problem.<br>> >><br>> >> I was not sure whether to use nexcl =2 or nexcl =3 in the case of<br>> >> scaled 1-4 interactions, but by trial and error I found that one<br>> >> should use nexcl =3, otherwise you have the full 1-4 interaction + the<br>> >> scaled one, so in total a scaling of 1.5 instead of 0.5.<br>> >><br>> >> Any ideas why gen-pairs = yes option is not working would be much<br>> >> appreciated.<br>> >><br>> >> Thanks to those who responded to my first email,<br>> >><br>> >> Mike<br>> >><br>> >><br>> >><br>> >> On Thu, Jul 2, 2009 at 6:54 PM, Mike Wykes<mikewykes@gmail.com> wrote:<br>> >> > Dear all<br>> >> ><br>> >> > I would like to simulate beta cyclodextrin in various organic<br>> >> > solvents with the OPLSAA FF for Carbohydrates (J Comput Chem 18:<br>> >> > 1955-1970, 1997) but am having problems with the short range Coulomb<br>> >> > and LJ interactions.<br>> >> > This FF (and OPLS in general) does not assign LJ parameters to<br>> >> > hydrogen atoms in OH groups, relying on the repulsion between oxygens<br>> >> > to keep the hydrogen (charge +0.435 ) of one OH group getting too<br>> >> > close to the O (charge -0.7 ) of another.<br>> >> > However in MD simulations, the hydrogen of one OH group collides with<br>> >> > the O of another, and shortly after the system explodes.<br>> >> ><br>> >> > Obviously, this could be a mistake of how I converted the parameters<br>> >> > in the paper into gromacs parameters, so I have checked this and found<br>> >> > no mistakes. Some of the parameters are taken from regular OPLS,<br>> >> > allowing me to check my conversion by comparing to the parameters in<br>> >> > gromacs/share/top/ffoplsaa*.itp files.<br>> >> ><br>> >> > Out of curiosity I implemented the same forcefield in the tinker md<br>> >> > package and the O...H system was stable during MD, with no O..H<br>> >> > collisions. Comparing the energies of exactly the same geometry of<br>> >> > beta cyclodextrin with the same OPLS parameters shows identical bonded<br>> >> > interactions, but differences in the non-bonded interactions:<br>> >> ><br>> >> > tinker(kcal/mol) gmx (kj/mol) gmx(kcal/mol)<br>> >> > difference<br>> >> > Total Potential energy 312 -1416.98 -338.67 650.67<br>> >> > Bond Stretching 23.32 97.58 23.32 0<br>> >> > Angle Bending 30.38 127.11 30.38 0<br>> >> > Torsional Angle 312.06 1305.64 312.06 0<br>> >> > Van der Waals 13.69 -119.03 -28.45 42.14<br>> >> > Charge-Charge -67.45 -2828.29 -675.98 608.52<br>> >> ><br>> >> > In both cases the molecule was in the gas phase, all non-bonded<br>> >> > interactions being treated with a cutoff of 1.5 nm.<br>> >> ><br>> >> > Any suggestions as to what could be going wrong in my gromacs<br>> >> > calculations would be much appreciated.<br>> >> ><br>> >> > Please find my mdp, top and itp files below. I am using version 4.0.5.<br>> >> ><br>> >> > Many thanks,<br>> >> ><br>> >> > Mike<br>> >> ><br>> >> ><br>> >> _______________________________________________<br>> >> gmx-users mailing list gmx-users@gromacs.org<br>> >> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> >> Please search the archive at http://www.gromacs.org/search before posting!<br>> >> Please don't post (un)subscribe requests to the list. Use the<br>> >> www interface or send it to gmx-users-request@gromacs.org.<br>> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> ><br>> > ________________________________<br>> > Express yourself instantly with MSN Messenger! MSN Messenger<br>> ><br>> > ________________________________<br>> > _______________________________________________<br>> > gmx-users mailing list gmx-users@gromacs.org<br>> > http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> > Please search the archive at http://www.gromacs.org/search before posting!<br>> > Please don't post (un)subscribe requests to the list. Use the<br>> > www interface or send it to gmx-users-request@gromacs.org.<br>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> ><br>> > ________________________________<br>> > Express yourself instantly with MSN Messenger! MSN Messenger<br>> > _______________________________________________<br>> > gmx-users mailing list gmx-users@gromacs.org<br>> > http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> > Please search the archive at http://www.gromacs.org/search before posting!<br>> > Please don't post (un)subscribe requests to the list. Use the<br>> > www interface or send it to gmx-users-request@gromacs.org.<br>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> ><br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br><br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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