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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