[gmx-users] QM/MM simulation: point-charge, pbc and bOPT=yes problems

Mark Abraham mark.j.abraham at gmail.com
Fri Aug 22 16:56:47 CEST 2014


Hi,

Unfortunately the QM/MM interface is completely unmaintained, so the fact
that it doesn't set fire to your chair is something of a bonus! If you can
get the group scheme to do something useful, that's great, but I would
suggest you build an older version of GROMACS.

In practice, with the impending death of the group scheme, QM/MM support
might disappear entirely, unless someone steps up to do the work!

Mark
On Aug 22, 2014 3:23 PM, "Bence Hégely" <hoemberr at gmail.com> wrote:

> Dear Gromacs users!
> I'm trying to interface gromacs (5.0) with orca (2.9.1), although i
> encountered some problems. I'm testing a tripeptide system which i found
> here: http://www.picb.ac.cn/~liwenjin/QMMM_simulations/index.html , but
> i'm
> using a different .mdp file, with these parameters (i copied the only
> working configuration):
> integrator          = steep
> dt                  =  0.002    ; ps !
> nsteps              =   10000
> nstlist             =  10
> ns_type             =  grid
> rlist               =  3.0
> rcoulomb            =  3.0
> coulombtype         = cut-off
> vdwtype             = cut-off
> rvdw                = 3.0
> pbc                 = no
> periodic_molecules  =  no
> constraints         = none
> energygrps          = QMatoms MMatoms
> cutoff-scheme       = group
>
> ; QM/MM calculation stuff
> QMMM = yes
> QMMM-grps = QMatoms
> QMmethod = rhf
> QMbasis = 3-21G
> QMMMscheme = normal
> QMcharge = 0
> QMmult = 1
> bOPT                     = no
> bTS                      = no
> SH                       = no
>
> ;
> ;       Energy minimizing stuff
> ;
> emtol               =  60   ; minimization thresold (kj/mol.nm-1)    1
> hartree/bohr= 49614.75241 kj/mol.nm-1  1 kj/mol.nm-1=2.01553e-5
> hartree/bohr
> emstep              =  0.01  ; minimization step in nm
>
> with the .ORCAINFO file of
> ! LDA cc-(p)VDZ
>
> %LJcoefficients "peptide.LJ"
>
> %pointcharges "peptide.pc"
>
> %geom
>
> end
>
> After i modified the ffnonbonded.itp and atomtypes.atp for the dummy atom,
> rebuilt the gromacs and the grompp and mdrun commands were executed with
> the following:
> grompp -p peptide.top -c peptide.gro -f peptide.mdp -n peptide.ndx -o
> peptide.tpr
> mdrun -s peptide.tpr -c peptide.gro -o peptide.trr -e peptide.edr -g
> peptide.log
>
> The first thing is, that the default neighbor searching algorithm -
> cutoff-scheme=verlet - isn't producing any point charges for ORCA and the
> job ends with a segmentation fault, although the group cutoff scheme works
> well. It is not clear to me why this is happening, but i suspect the
> problem lies in that the qm/mm subrutines are quite old (~2003?), and the
> verlet scheme introduced much later in gromacs 4.6 (2013).
>
> The second problem that i have encountered is with the pbc options: if i'm
> using pbc=xyz the job terminates with a segmentation fault (core dumped)
> after orca terminates normally. After i looked for some explanation about
> coordinate updating on the qmmm.c source file I saw some comments that the
> update_QMMMrec function not working properly without pbc, even though it
> works just fine with pbc=no. Little bit confused of that, although the
> gromacs was tested on the regression package and all the tests passed.
>
> The third problem is with the bOPT = yes option. When i pass the
> optimization to the orca, after the first optimization cycle (before orca
> terminates normally)  the tripeptide's qm region forms an unrealistic
> geometry. At the input of the second orca run, the qm region scatters, the
> atoms move apart around 10 angströms from each other and gives the
> following error message:
> Error (ORCA_GSTEP): The lambda equations have not converged
>
> although, the job continues and at the third orca run gives the following:
> Calling '/export/home/hegely/Programz/orca_2_9_1_linux_x86-64/orca
> peptide.inp >> peptide.out'
>
> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
> !!!                        FATAL ERROR ENCOUNTERED               !!!
> !!!                        -----------------------               !!!
> !!!                          I/O OPERATION FAILED                !!!
> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
> ABORTING THE RUN
>
> and the job runs onward, giving the same error message over and over until
> i kill it. In the gromacs .log file no error messages are presented and i
> don't really have a clue of what's going on. Maybe the point charges
> destroy the geometry of the peptide?
>
> I think i checked all the qm/mm, orca searching results in the gmx-users
> list, but didn't find the solutions. Sorry if i missed something out, but i
> would appreciate any help!
>
> Bence Hégely
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