Dear GMX code writters,
Could anyone tell me why this comments in the code *mdlib/qmmm.c
appear*?(version 4.5.3)
at *line ~ 714*, in the beginning of subroutine* update_QMMMrec*
======================================================
*/* updates the coordinates of both QM atoms and MM atoms and stores
* them in the QMMMrec.
*
* NOTE: is NOT yet working if there are no PBC. Also in ns.c, simple
* ns needs to be fixed!
*/*
======================================================
First of all, I have a non-PBC job with electronic embedding and it
fails right in this routine. So I guess this is the reason, for non-PBC, it
crashes. But for oniom, it went through. Is there any simple fix to have the
non-PBC qmmm work? I'm also interested in doing non-PBC calculation(large
cluster).
Xiaohu
On Thu, Jan 27, 2011 at 9:11 AM, Christoph Riplinger
<c...@thch.uni-bonn.de>wrote:
> 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
>
>
>
--
=================================================
Xiaohu Li
Post-doctoral Research Associate
Department of Chemistry
Northwestern University
2145 Sheridan Road
Evanston IL 60208
U.S.A
=================================================
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