GMX + ORCA QM/MM

[Frank Uhlig]

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

[Gerrit Groenhof]

Hi,

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

Gerrit

Post by Frank Uhlig
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
--without-qmmm-orca Use ORCA for QM-MM
and the respective for the other three possible programs for QM/MM
calculations...
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

[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

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
--without-qmmm-orca Use ORCA for QM-MM
and the respective for the other three possible programs for QM/MM
calculations...
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