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
