Dear Mark,
Thank you for your reply. Unfortunately, TIP5P is completely rigid and
the FLEXIBLE define will not change it. Any other ideas?
Best,
g
On 2013-09-24 23:51, Mark Abraham wrote:
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 <g...@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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