Dear Gigo: everything that I suggested was just ways that you might get a system without bad contacts to start your simulation with the proper (standard) tip5p model and oplsaa. I expected that combination to work together since they came out of the same lab, but looking at the initial tip5p paper, they didn't test with protein in that first work. I thought that perhaps you had some bad clashes that simply could not be removed with EM using a rigid water model (I have seen that sometimes even with tip3p).
I just checked and the tip5p sigmas and epsilons in gromacs are correct. Also, tip5p has been used successfully with the charmm foce field: http://pubs.acs.org/doi/abs/10.1021/ct700053u However, it does appear that oplsaa-x (including new halogen parameters) can not be used with tip5p: http://pubs.acs.org/doi/abs/10.1021/ct300180w due to the exact problem that you are noting: "Thus, the present OPLS-AAx model should not be used with TIP5P water,(7d) as the X-sites and water lone-pair sites can fuse; there is no problem with TIP3P and TIP4P, as the negative charge is shielded by the Lennard-Jones sphere centered on the oxygen atom.(14) If needed, the issue can be avoided by the introduction of small Lennard-Jones parameters for the X-sites." Are you using halogens with oplsaa-x? Standard oplsaa (non-x) and tip5p seem to be a fine combination: http://www.sciencedirect.com/science/article/pii/S0006349507713863 you might want to contact the authors of that paper to see if they ever had such problems. Chris. Dear Chris, Thank you for your reply. I defined a new virtual atomtype (type D) with LJ sigma 1.72A ( 2*0.7+1.72=3.12, which is sigma of the oxygen) and played a bit with epsilon till the new LJ repulsion was able to prevent the build up of a huge force on the oxygen while interacting with dimensionless charged hydrogens. Also, I copied the flexibility parameters from tip4p to see if it helps in minimization before I turn it into rigid water - it seems that it does. I was able to minimize the system with such water. Also, I minimized the system with tip4p and replaced it with tip5p with a script. I tried to minimize the system afterwards with true tip5p, which did not work. My question is, besides the correctness of water model, why do you think it is safe to remove the LJ on lone electron pairs in MD? Will it not collapse like in energy minimization? Best Regards, Grzegorz -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
