[gmx-developers] GMX + ORCA QM/MM

Gerrit Groenhof ggroenh at gwdg.de
Wed Jul 13 11:16:31 CEST 2011


I am on vacation actually. Although it looks like a gmx problem,  I 
forward this email to Cristoph Riplinger, who did the orca interface.


On 07/13/2011 10:08 AM, Frank Uhlig wrote:
> Dear gmx-developers,
> 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

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