[gmx-users] OPLS/AA + TIP5P, anybody?
chris.neale at mail.utoronto.ca
Sat Sep 28 17:29:42 CEST 2013
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:
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:
you might want to contact the authors of that paper to see if they ever had such problems.
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
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