[gmx-users] Gromacs-Orca QMMM LJ coefficients problem

minws minmatsoukas at gmail.com
Tue Jul 17 13:27:55 CEST 2012


I've been trying some time now to run a QMMM calculation with gromacs and
orca on a system of 5000 atoms with the QM system being ~300 atoms.

Setting up the calculation with bOpt = yes and 1 minim step in the .mdp file
produces some problems. 

Orca does the calculation without taking into account the LJ coefficients.
The .LJ file should be generated by gromacs prior to the calculation so Orca
uses it for the QM atoms optimization right? ( I have seen that there should
be LJ and LJ.Excl files) 

However these files are not generated and Orca does a "perfect" optimization
of 300 cycles but without taking into account any Lennard Jones input. So in
every optimization step Orca skips VdW correction (No LJ-filename given...
skipping VDW correction) because it doesn't find the LJ file and continues
the QM optimization in the absence of the MM system.

I am running gromacs 4.5.5 and after many many tries, I cannot see the .LJ
file. Not in the beginning, nor during the calculation in the woking
directory. Could there be an explanation why gromacs does not generate this


I attach my mdp file:
title               =  Yo			; a string
cpp                 =  /lib/cpp			; c-preprocessor
integrator          =  cg 			;
;integrator               = l-bfgs

rlist               =  1.0 			; cut-off for ns
rvdw                =  1.4 			; cut-off for vdw
rcoulomb            =  1.5 			; cut-off for coulomb

;       Energy minimizing stuff
nsteps              =  1
emtol               =  100
emstep              =  0.1
nstxout                  = 1
nstfout                  = 1
nstlog                   - 1
nstvout                  = 1
nstxtcout                = 1
nstenergy                = 1

QMMM                     = yes
QMMM-grps                = QMatoms
QMMMscheme               = ONIOM
QMbasis                  = 6-31g* 
QMmethod                 = RHF 
QMcharge                 = 1
QMmult                   = 1
bOpt                     = yes

and ORCAINFO file:
! RHF 6-31g* SV(P) moread
%moinp "orbitals.gbw"
%pointcharges "charges.pc"
%pal nprocs 24

and the .inp file Orca needs that is generated by gromacs:
#input-file generated by gromacs
! RHF 6-31g* SV(P) moread
%moinp "orbitals.gbw"
%pointcharges "charges.pc"
%pal nprocs 24

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