<quote who="Mark Abraham"> > Nicolas SAPAY wrote: >> good remark... here is the files! I precise that modifying the inter-atomic distance doesn't solve the problem and that nb parameters are >> defined in the ffcharm27nb.itp file as follow : >> >> [ atomtypes ] >> OT 15.9994 0.000 A 2.489540e-03 2.434767e-06 >> HT 1.0080 0.000 A 3.153970e-09 1.292128e-17 >> >> [ nonbond_params ] >> OT HT 1 4.382447e-05 1.371950e-09 > > Well the good news is that my CHARMM27 implementation agrees with these C6 and C12 values... for reference, I use these with > > [ defaults ] > ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ > 1 1 yes 1.0 1.0 > > and see no problems. > >> [ pairtypes ] >> OT HT 1 4.382447e-05 1.371950e-09 > > This shouldn't be needed, but won't be causing problems. > > I can't see anything wrong with your .top or .mdp files. > > The V and W values in the [ atomtypes ] section won't be being used, because of the existence of this defined interaction in [ nonbond_params > ], so you can test that that's correct by zeroing these values and looking for no change in the output. They look wrong, though, and certainly don't combine using comb-rule 1 to give the correct values.
> Mark > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > 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 > > I'm absolutely agree to say that LJ parameters given in the [ atomtypes ] section cannot give the correct results when using the combination rule 1. The Gromacs manual say for comb-rule 1: Vii = Ci(6) = 4 * ei * si^6 Wii = Ci(12) = 4 * ei * si^12 and then: Cij(6) = (Ci(6) * Ci(6))^1/2 Cij(12) = (Ci(12) * Ci(12))^1/2 This assumes that sij = (si * sj)^1/2 while in CHARMM sij = si/2 + sj/2. I have tried to used the comb-rule 2 of Gromacs to fix that. Unfortunately, I obtain an error each time I used grompp when I define a [ nonbond_params ]("Trying to add Buck.ham(SR) while the default nonbond type is LJ (SR)"). Additionally, I obtain wrong energy values. So, I have switched back to comb-rule 1 and [ nonbond_params ]. I have also tried to nullify OT and HT parameters in [ atomtypes ] (with comb-rule 1 and defined [ nonbond_params ]). No modification happened, as expected. However, I frequently obtain this kind of message when working on simple systems made of 2 atoms: "Can not invert matrix, determinant = " Together with the fact that I obtain a kinetic energy of 0.00 make me think that a variable is not initialized or something like that... I'm still puzzled. Nicolas -- [ Nicolas Sapay Ph.D. ] University of Calgary, Dept. of Biological Sciences 2500 University Dr. NW, Calgary AB, T2N 1N4, Canada Tel: (403) 220-6869 Fax: (403) 289-9311 _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users 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
