Dear Jose,
I just installed the 4.5.5. version and the calculation runs ok for me!
But I did change the ORCAINFO file:
First of all you should clean your ORCAINFO file. Remove
!QMMMOpt COPT
and remove
!EnGrad
Otherwise the program might get confused about doing a single point and
gradient calculation only. I.e. as stated in the manual, you should only
give information on the electronic structure calculation method and
basis set in the ORCAINFO file. Gromacs itself will put the
!QMMMOpt
keyword, if you request
bOpt = yes
Otherwise Gromacs puts
!EnGrad
Furthermore, you chose !COPT in the ORCAINFO file. Do you want to have
the optimization done in cartesian coordinates? I would suggest you do
the optimization in internal coordinates. This runs usually faster. Did
you try the optimization in internal coordinates?
Hope that helps,
Christoph
On 11/22/2011 04:25 PM, Jose Tusell wrote:
I'm using GROMACS 4.5.5. Here is my minim.mdp file:
; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest descent
minimization)
emtol = 500.0 ; Stop minimization when the maximum
force< 1000.0 kJ/mol/nm
emstep = 0.01 ; Energy step size
nsteps = 50000 ; Maximum number of (minimization)
steps to perform
; Parameters describing how to find the neighbors of each atom and how
to calculate the interactions
nstlist = 1 ; Frequency to update the neighbor
list and long range forces
ns_type = grid ; Method to determine neighbor list
(simple, grid)
rlist = 1.0 ; Cut-off for making neighbor list
(short range forces)
coulombtype = PME ; Treatment of long range
electrostatic interactions
rcoulomb = 1.0 ; Short-range electrostatic cut-off
rvdw = 1.0 ; Short-range Van der Waals cut-off
pbc = xyz ; Periodic Boundary Conditions (yes/no)
nstxout = 10 ; save coordinates every 0.2 ps
nstvout = 10 ; save velocities every 0.2 ps
nstenergy = 10 ; save energies every 0.2 ps
nstlog = 10 ; update log file every 0.2 ps
QMMM = yes
QMMM-grps = Other
QMmethod = RHF
QMbasis = 3-21G
QMMMscheme = Normal
QMcharge = -2
QMmult = 1
SH = no
bOpt = yes
bTS = no
Here is my ORCAINFO file:
!PAL8 Quick-DFT VerySlowConv TightSCF KDIIS VDW EnGrad NoUseSym
!QMMMOpt COPT
%scf
Maxiter 5000
end
%pal nprocs 8
end
I think that all you need to reproduce the error. Let me know what you find.
Thanks for you input,
Jose R Tusell
On Tue, Nov 22, 2011 at 8:06 AM, Christoph Riplinger
<c...@thch.uni-bonn.de> wrote:
Dear Jose,
Also our calculations using bOpt with ORCA are fine.
ORCA does not give the coordinates in nm, but in Angstrom.
Which version of gromacs are you using?
Christoph
On 11/22/2011 03:53 PM, Jose Tusell wrote:
When GROMACS takes care of the optimization this doesn't happen.
Jose R Tusell
On Tue, Nov 22, 2011 at 12:35 AM, Gerrit Groenhof<ggro...@gwdg.de> wrote:
On 11/22/2011 04:02 AM,gmx-users-requ...@gromacs.org wrote:
gmx-users@gromacs.org
To subscribe or unsubscribe via the World Wide Web, visit
2. Re: GROMACS/ORCA QMMM (Jose Tusell)
Does anyone know what is going on with the coordinates of the QM
region? Why are they not converted to the correct units? Could
anyone point me to the error?
I have not experienced this myself. The only thing I can think of is that
ORCA returns the atom coordinates in nm?
Does this happen also when you let Gromacs take care of the optimization?
Gerrit
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