<p>Hey,</p>
<p>sorry for the late reply. I ran a few tests and it works perfectly fine.</p>
<p>Thanks again,</p>
<p>Frank</p>
<p>On Wed, Jul 13, 2011 at 12:03 PM, Gerrit Groenhof <<a href="mailto:ggroenh@gwdg.de">ggroenh@gwdg.de</a>> wrote:<br>
> I had a look anyway.<br>
><br>
> On grompp: Since 4.0, the QM atoms need to be in one topology file. Thus if<br>
> you have 6 water, you need an atoms section with 6 waters. Dividing the QM<br>
> atoms over multiple topologies does not work. see below.<br>
><br>
> On mdrun, the above problem works with gmx/gaussian. I never worked with<br>
> gmx/orca before, but frmo the gromacs side there seems no problem anymore.<br>
><br>
> Hope this helps.<br>
><br>
> Best wishes,<br>
><br>
> Gerrit<br>
><br>
><br>
> ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;<br>
> ; defaults and all atom types ;<br>
> ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;<br>
><br>
> [ defaults ]<br>
> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ<br>
> 1 2 yes 1.0 1.0<br>
><br>
> [ atomtypes ]<br>
> ; name mass charge ptype sigma epsilon<br>
> OW 8 16.0 -0.8476 A 0.3165492 0.650299<br>
> HW 1 1.0 0.4238 A 0.0 0.0<br>
><br>
> ;;;;;;;;;;;;;;;<br>
> ; SPC/E water ;<br>
> ;;;;;;;;;;;;;;;<br>
><br>
> [ moleculetype ]<br>
> ; molname nrexcl<br>
> SOL 1<br>
><br>
> [ atoms ]<br>
> ; nr type resnr residue atom cgnr charge mass<br>
> 1 OW 1 SOL OW 1 -0.8476<br>
> 2 HW 1 SOL HW1 1 0.4238<br>
> 3 HW 1 SOL HW2 1 0.4238<br>
><br>
> [ settles ]<br>
> ; OW funct doh dhh<br>
> 1 1 0.1 0.1633<br>
><br>
> [ exclusions ]<br>
> 1 2 3<br>
> 2 1 3<br>
> 3 1 2<br>
><br>
> [ moleculetype ]<br>
> ; molname nrexcl<br>
> QM 1<br>
><br>
> [ atoms ]<br>
> ; nr type resnr residue atom cgnr charge mass<br>
> 1 OW 1 QM OW 1 -0.8476<br>
> 2 HW 1 QM HW1 1 0.4238<br>
> 3 HW 1 QM HW2 1 0.4238<br>
> 4 OW 1 QM OW 1 -0.8476<br>
> 5 HW 1 QM HW1 1 0.4238<br>
> 6 HW 1 QM HW2 1 0.4238<br>
> 7 OW 1 QM OW 1 -0.8476<br>
> 8 HW 1 QM HW1 1 0.4238<br>
> 9 HW 1 QM HW2 1 0.4238<br>
> 10 OW 1 QM OW 1 -0.8476<br>
> 11 HW 1 QM HW1 1 0.4238<br>
> 12 HW 1 QM HW2 1 0.4238<br>
> 13 OW 1 QM OW 1 -0.8476<br>
> 14 HW 1 QM HW1 1 0.4238<br>
> 15 HW 1 QM HW2 1 0.4238<br>
> 16 OW 1 QM OW 1 -0.8476<br>
> 17 HW 1 QM HW1 1 0.4238<br>
> 18 HW 1 QM HW2 1 0.4238<br>
><br>
> [ system ]<br>
> something weird<br>
><br>
> [ molecules ]<br>
> QM 1<br>
> SOL 58<br>
><br>
> On 07/13/2011 10:08 AM, Frank Uhlig wrote:<br>
>><br>
>> Dear gmx-develo11pers,<br>
>><br>
>> I have a few comments concerning QM/MM in Gromacs in conjunction with<br>
>> Orca. I am using the latest Gromacs version 4.5.4 and the latest Orca<br>
>> version 2.8.0 to perform QM/MM calculations.<br>
>><br>
>> 1) it is a bit misleading that in the help of the configure script it<br>
>> is written:<br>
>><br>
>> --without-qmmm-orca Use ORCA for QM-MM<br>
>><br>
>> and the respective for the other three possible programs for QM/MM<br>
>> calculations...<br>
>><br>
>> 2) I followed the instructions on this webpage:<br>
>><br>
>> <a href="http://wwwuser.gwdg.de/~ggroenh/qmmm.html">http://wwwuser.gwdg.de/~ggroenh/qmmm.html</a><br>
>><br>
>> --> this means ./configure --with-qmmm-orca --without-qmmm-gaussian<br>
>><br>
>> to build a QM/MM version of GMX together with Orca. The build goes<br>
>> fine and seems to work...<br>
>><br>
>> I also tried to build the GMX/ORCA-QM/MM version via CMake (i.e.,<br>
>> ccmake). Although I activated "orca" as GMX_QMMM_PROGRAM in the gui<br>
>> and (re-)configured, the variable GMX_QMMM_ORCA does not get set in<br>
>> the src/config.h file. Thus, the obtained build will not work for<br>
>> QM/MM calculations...<br>
>><br>
>> 3) If I configure gromacs as described in the first part of 2) above I<br>
>> obtain a version that seems to work at first. After some experimenting<br>
>> with the general setup I encountered some problems though. I attached<br>
>> all files necessary files to illustrate and reproduce those problems.<br>
>><br>
>> When putting the QM residues first in the [ molecules ] section in the<br>
>> topology file, grompp fails with a segmentation fault.<br>
>> When putting the QM residues last in the [ molecules ] section in the<br>
>> topology file, mdrun fails with a segmentation fault (mdrun -nt 1)<br>
>> before calling Orca.<br>
>> When putting the QM residues (and all the other residues) in a<br>
>> disordered fashion in the topology file (and not the QM<br>
>> residues first or last) the calculations runs just fine.<br>
>><br>
>> The included examples all contain the same configuration. They only<br>
>> differ in the order of the residues in the conf.gro, topol.top and<br>
>> index.ndx files.<br>
>><br>
>> I also included the debug information for the two failing tests. I am<br>
>> not too familiar with C, so I would appreciate your help. If you have<br>
>> any suggestion on how to fix these issues or at least further<br>
>> information on where they are stemming from, please let me know.<br>
>><br>
>> Best regards and thanks in advance,<br>
>><br>
>> Frank<br>
><br>
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</p>