[gmx-developers] GMX + ORCA QM/MM

[Gerrit Groenhof]

  I had a look anyway.

On grompp: Since 4.0, the QM atoms need to be in one topology file. Thus 
if you have 6 water, you need an atoms section with 6 waters. Dividing 
the QM atoms over multiple topologies does not work. see below.

On mdrun, the above problem works with gmx/gaussian. I never worked with 
gmx/orca before, but frmo the gromacs side there seems no problem anymore.

Hope this helps.

Best wishes,

Gerrit


;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
; defaults and all atom types ;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

[ defaults ]
; nbfunc   comb-rule   gen-pairs   fudgeLJ   fudgeQQ
   1        2           yes         1.0       1.0

[ atomtypes ]
; name   mass     charge     ptype   sigma       epsilon
   OW   8  16.0     -0.8476    A       0.3165492   0.650299
   HW   1   1.0      0.4238    A       0.0         0.0

;;;;;;;;;;;;;;;
; SPC/E water ;
;;;;;;;;;;;;;;;

[ moleculetype ]
; molname   nrexcl
   SOL       1

     [ atoms ]
     ; nr   type   resnr   residue   atom   cgnr   charge    mass
       1    OW     1       SOL       OW     1      -0.8476
       2    HW     1       SOL       HW1    1       0.4238
       3    HW     1       SOL       HW2    1       0.4238

     [ settles ]
     ; OW   funct   doh   dhh
       1    1       0.1   0.1633

     [ exclusions ]
     1   2   3
     2   1   3
     3   1   2

[ moleculetype ]
; molname   nrexcl
    QM       1

     [ atoms ]
     ; nr   type   resnr   residue   atom   cgnr   charge    mass
       1    OW     1       QM        OW     1      -0.8476
       2    HW     1       QM        HW1    1       0.4238
       3    HW     1       QM        HW2    1       0.4238
       4    OW     1       QM        OW     1      -0.8476
       5    HW     1       QM        HW1    1       0.4238
       6    HW     1       QM        HW2    1       0.4238
       7    OW     1       QM        OW     1      -0.8476
       8    HW     1       QM        HW1    1       0.4238
       9    HW     1       QM        HW2    1       0.4238
      10    OW     1       QM        OW     1      -0.8476
      11    HW     1       QM        HW1    1       0.4238
      12    HW     1       QM        HW2    1       0.4238
      13    OW     1       QM        OW     1      -0.8476
      14    HW     1       QM        HW1    1       0.4238
      15    HW     1       QM        HW2    1       0.4238
      16    OW     1       QM        OW     1      -0.8476
      17    HW     1       QM        HW1    1       0.4238
      18    HW     1       QM        HW2    1       0.4238

[ system ]
something weird

[ molecules ]
QM          1
SOL        58

On 07/13/2011 10:08 AM, Frank Uhlig wrote:
> Dear gmx-develo11pers,
>
> I have a few comments concerning QM/MM in Gromacs in conjunction with
> Orca. I am using the latest Gromacs version 4.5.4 and the latest Orca
> version 2.8.0 to perform QM/MM calculations.
>
> 1) it is a bit misleading that in the help of the configure script it
> is written:
>
> --without-qmmm-orca     Use ORCA for QM-MM
>
> and the respective for the other three possible programs for QM/MM
> calculations...
>
> 2) I followed the instructions on this webpage:
>
> http://wwwuser.gwdg.de/~ggroenh/qmmm.html
>
> -->  this means ./configure --with-qmmm-orca --without-qmmm-gaussian
>
> to build a QM/MM version of GMX together with Orca. The build goes
> fine and seems to work...
>
> I also tried to build the GMX/ORCA-QM/MM version via CMake (i.e.,
> ccmake). Although I activated "orca" as GMX_QMMM_PROGRAM in the gui
> and (re-)configured, the variable GMX_QMMM_ORCA does not get set in
> the src/config.h file. Thus, the obtained build will not work for
> QM/MM calculations...
>
> 3) If I configure gromacs as described in the first part of 2) above I
> obtain a version that seems to work at first. After some experimenting
> with the general setup I encountered some problems though. I attached
> all files necessary files to illustrate and reproduce those problems.
>
> When putting the QM residues first in the [ molecules ] section in the
> topology file, grompp fails with a segmentation fault.
> When putting the QM residues last in the [ molecules ] section in the
> topology file, mdrun fails with a segmentation fault (mdrun -nt 1)
> before calling Orca.
> When putting the QM residues (and all the other residues) in a
> disordered fashion in the topology file (and not the QM
> residues first or last) the calculations runs just fine.
>
> The included examples all contain the same configuration. They only
> differ in the order of the residues in the conf.gro, topol.top and
> index.ndx files.
>
> I also included the debug information for the two failing tests. I am
> not too familiar with C, so I would appreciate your help. If you have
> any suggestion on how to fix these issues or at least further
> information on where they are stemming from, please let me know.
>
> Best regards and thanks in advance,
>
> Frank