[gmx-developers] GMX + ORCA QM/MM

[Frank Uhlig]

Hey,

sorry for the late reply. I ran a few tests and it works perfectly fine.

Thanks again,

Frank

On Wed, Jul 13, 2011 at 12:03 PM, Gerrit Groenhof <ggroenh at gwdg.de> wrote:
>  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
>
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