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 > -- > 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 -- 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
