[gmx-users] QMMM with ORCA

Xiaohu Li xiaohuli914 at gmail.com
Wed Jan 26 06:48:06 CET 2011

Hi, All,
     I'm trying to see if anybody has experience of using the interface of
gromacs and ORCA(since it's free). I know that the following link gave
information on how
     But.....But, the gromacs in the above link is quite old(3.2). I
download the latest 4.5.3 and followed the instructions in the above link
and I was trying to optimize an simple cluster(no pbc) where part of it are
treated using QM. here is the example mdp file
title               =  cpeptide
integrator          =  steep   ;integrator includes energy minimization
dt                  =  0.002    ; ps !
nsteps              =   10000
nstlist             =  1
ns_type             =  simple
rlist               =  3.0
rcoulomb            =  3.0
coulombtype         = cut-off
vdwtype             = cut-off
rvdw                = 3.0
pbc                 =  no
periodic_molecules  =  no
constraints         = none
energygrps          = qm_part mm_part
; QM/MM calculation stuff
QMMM = yes
QMMM-grps = qm_part
QMmethod = rhf
QMbasis = 3-21G
QMMMscheme = oniom
QMcharge = 0
QMmult = 1
;       Energy minimizing stuff
emtol               =  60   ; minimization thresold (kj/mol.nm-1)    1
hartree/bohr= 49614.75241 kj/mol.nm-1  1 kj/mol.nm-1=2.01553e-5 hartree/bohr
emstep              =  0.01  ; minimization step in nm
I set up the BASENAME and ORCA_PATH as told in the instruction.
first of all, the normal electronic embedding just simply gave segmentation
fault error right after the it prints information on number of steps of

So I switch to ONIOM, this time, at least, orca is called and energy and
gradient are both generated. However, when it comes to read the energy and
gradient, it always crashes when tried to read gradient, this is at *line
346* source code src/mdlib/qm_orca.c
sscanf(buf,"%lf\n", &QMgrad[k][XX]);
a segmentation fault error is printed. If I replace the &QMgrad[k][XX] by an
temporary variable temp
 sscanf(buf,"%lf\n", &temp);
temp gets the correct value and if I use,
and tries to print QMgrad[k][XX], a bus error will be printed.
I did some research online, seems that usually this implies an memory bug in
the code which is the most difficult bug one can ever encounter.
So has anyone successfully used gromacs and orca to do QMMM?
Generally, would anyone recommend using gromacs to do QMMM?

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