[gmx-users] QMMM with ORCA

[Christoph Riplinger]

Hi Xiaohu,

We are using gromacs/ORCA quite a lot. It works like any of the other 
interfaced programs and whether you should use it depends on your needs 
to the QM part of the QM/MM calculation.

I am using gromacs 4.0.7, but I downloaded the 4.5.3 version to test it.

I could not reproduce your problem with ONIOM. For the electrostatic 
embedding bug, I agree. This didn't work in my test calculation, but my 
gdb told me that the abort occured before the qm_orca.c was even called. 
I suspect the bug is in the general qmmm.c code. I do not have access to 
the other QM-programs and cannot test this, so if you have, could you 
please run the same job with a different QM-program.

Hope that helps

Christoph



On 01/26/2011 06:48 AM, Xiaohu Li wrote:
> 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
> http://wwwuser.gwdg.de/~ggroenh/qmmm.html#code 
> <http://wwwuser.gwdg.de/%7Eggroenh/qmmm.html#code>
>      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 algorithms
> 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 optimization.
>
> 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,
> QMgrad[k][XX]=temp
> 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?
>
> Cheers,
> Xiaohu

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