[gmx-users] 2. Re: GROMACS/ORCA QMMM (Jose Tusell)
cri at thch.uni-bonn.de
Thu Nov 24 17:59:23 CET 2011
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
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
keyword, if you request
bOpt = yes
Otherwise Gromacs puts
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,
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
> 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
> Maxiter 5000
> %pal nprocs 8
> 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
> <cri at 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?
>> 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<ggroenh at gwdg.de> wrote:
>>>> On 11/22/2011 04:02 AM,gmx-users-request at gromacs.org wrote:
>>>>> gmx-users at 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?
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