[gmx-users] OPLS/AA + TIP5P, anybody?

[Mark Abraham]

You should be able to minimize with CG and TIP5P by eliminating
constraints, by making the water use a flexible molecule, e.g. define
= -DFLEXIBLE (or something). Check your water .itp file for how to do
it.

Mark

On Tue, Sep 24, 2013 at 10:25 PM, gigo <gigo at ibb.waw.pl> wrote:
> Dear GMXers,
> Since I am interested in interactions of lone electron pairs of water oxygen
> within the active site of an enzyme that I work on, I decided to give TIP5P
> a shot. I use OPLSAA. I run into troubles very fast trying to minimize
> freshly solvated system. I found on the gmx-users
> (http://lists.gromacs.org/pipermail/gmx-users/2008-March/032732.html) that
> cg and constraints don't go together when TIP5P is to be used - thats OK. It
> turned out, however, that I was not able to minimize my protein even with
> steepest descent. The system minimizes with TIP4P pretty well (emtol=1.0).
> In the meantime I tried to minimize short peptide - 10aa, did not work as
> well. What happens? The LP of water used to get too close to positively
> charged hydrogens (without VDW radius) on arginine. It looks like this:
>
> Step=  579, Dmax= 8.0e-03 nm, Epot= -1.40714e+05 Fmax= 1.20925e+04, atom=
> 171
> Step=  580, Dmax= 9.6e-03 nm, Epot= -1.41193e+05 Fmax= 8.13923e+04, atom=
> 171
> Step=  581, Dmax= 1.1e-02 nm, Epot= -1.43034e+05 Fmax= 1.03648e+06, atom=
> 11181
> Step=  585, Dmax= 1.7e-03 nm, Epot= -1.46878e+05 Fmax= 4.23958e+06, atom=
> 11181
> Step=  587, Dmax= 1.0e-03 nm, Epot= -1.49565e+05 Fmax= 9.43285e+06, atom=
> 11181
> Step=  589, Dmax= 6.2e-04 nm, Epot= -1.59042e+05 Fmax= 3.55920e+07, atom=
> 11181
> Step=  591, Dmax= 3.7e-04 nm, Epot= -1.69054e+05 Fmax= 7.79944e+07, atom=
> 11181
> Step=  593, Dmax= 2.2e-04 nm, Epot= -1.85575e+05 Fmax= 2.27640e+08, atom=
> 11181
> Step=  595, Dmax= 1.3e-04 nm, Epot= -2.35034e+05 Fmax= 5.88938e+08, atom=
> 17181
> Step=  597, Dmax= 8.0e-05 nm, Epot= -2.39154e+05 Fmax= 1.22615e+09, atom=
> 11181
> Step=  598, Dmax= 9.6e-05 nm, Epot= -2.67157e+05 Fmax= 1.96782e+09, atom=
> 11181
> Step=  600, Dmax= 5.8e-05 nm, Epot= -4.37260e+05 Fmax= 1.08988e+10, atom=
> 11181
> Step=  602, Dmax= 3.5e-05 nm, Epot= -4.65654e+05 Fmax= 1.29609e+10, atom=
> 11181
> Step=  604, Dmax= 2.1e-05 nm, Epot= -1.17945e+06 Fmax= 1.31028e+11, atom=
> 11181
> Step=  607, Dmax= 6.3e-06 nm, Epot= -3.07551e+06 Fmax= 6.04297e+11, atom=
> 11181
> Step=  610, Dmax= 1.9e-06 nm, Epot= -4.26709e+06 Fmax= 1.61390e+12, atom=
> 11181
> Step=  611, Dmax= 2.3e-06 nm, Epot= -4.39724e+06 Fmax= 2.14416e+12, atom=
> 11181
> Step=  613, Dmax= 1.4e-06 nm, Epot= -1.27489e+07 Fmax= 1.03223e+13, atom=
> 17181
> Step=  614, Dmax= 1.6e-06 nm, Epot= -5.23118e+06 Fmax= 3.18465e+12, atom=
> 11181
> Energy minimization has stopped, but the forces havenot converged to the
> (...)
>
> In this example atom 171 is HH21 of ARG, and 11181 is oxygen of water that
> got close to this ARG. Sometimes the epot turns nan at the end. If you would
> like to reproduce, I put the peptide.pdb, the mdp file and the running
> script at http://shroom.ibb.waw.pl/tip5p . If anybody have any suggestions
> how to minimize (deep) with OPLSAA + TIP5P in gromacs (4.6.3 preferably...)
> without constraining bond lengths (which is also problematic), I will be
> very very grateful.
> Best,
>
> Grzegorz Wieczorek
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