[gmx-users] Re: gmx-users Digest, Vol 92, Issue 56

[Gerrit Groenhof]

Does this also happen if you use pbc?
gerrit
On 10 Dec 2011, at 10:59, gmx-users-request at gromacs.org wrote:

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> Today's Topics:
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>   1. qm/mm(orca/gromacs) (li yan)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Sat, 10 Dec 2011 17:59:11 +0800
> From: li yan <yanbochen123 at gmail.com>
> Subject: [gmx-users] qm/mm(orca/gromacs)
> To: gmx-users at gromacs.org
> Message-ID:
> 	<CAAsMsb+SwoEnh3o6vrVO_HJbw_MtqjO2w0vDjK4HsO3BbdOZ1Q at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Dear Gromacs developers:
> 
> I'm trying to run a QM-MM single point energy calculation on a
> structure (a small molecule with 50 water molecules with no pbc, no
> cutoff). I use orca for QM part amd gromacs for MM part. But when I
> run mdrun -nt 1 -s sp.tpr -c sp.gro -g sp.log, the ORCA run quickly
> and terminate naormally, but after that mdrun run stops with a
> segmentation fault. Here is the error information:
> 
> Back Off! I just backed up sp.log to ./#sp.log.1#
> 
> Reading file sp.tpr, VERSION 4.5.5 (single precision)
> 
> QM/MM calculation requested.
> 
> there we go!
> 
> Layer 0
> 
> nr of QM atoms 9
> 
> QMlevel: MP2/3-21G
> 
> /home/user/orca_x86_64_exe_r2360/home/user/programs/orca_x86_64_exe_r2360...
> 
> orca initialised...
> 
> Back Off! I just backed up traj.trr to ./#traj.trr.1#
> 
> Back Off! I just backed up ener.edr to ./#ener.edr.1#
> 
> starting mdrun 'Protein'
> 
> 0 steps,      0.0 ps.
> 
> Calling '/home/li/programs/orca_x86_64_exe_r2360/orca
> /home/li/Test/test_gmx/qmmm/test/sp.inp >>
> /home/li/Test/test_gmx/qmmm/test/sp.out'
> 
> Segmentation fault
> 
> Here is my sp.mdp
> 
> title                    = test
> 
> cpp                      =/lib/cpp
> 
> integrator               = md
> 
> nsteps                   = 0
> 
> dt                       = 0.001
> 
> ;constraints             = none
> 
> emtol                    = 10.0
> 
> emstep                   = 0.01
> 
> nstcomm                  = 1
> 
> ns-type                  = simple
> 
> nstlist                  = 0
> 
> rlist                    = 0
> 
> rcoulomb                 = 0
> 
> rvdw                     = 0
> 
> tcoupl                   = no
> 
> pcoupl                   = no
> 
> gen-vel                  = no
> 
> nstxout                  = 1
> 
> nstlog                   = 1
> 
> nstenergy                = 1
> 
> nstvout                  = 1
> 
> nstfout                  = 1
> 
> pbc                      = no
> 
> comm_mode                = angular
> 
> ; non-equilibrium md
> 
> freezegrps               = System
> 
> freezedim                = y y y
> 
> xtc_grps                 = System
> 
> energygrps               = System
> 
> ;qmmm calculation
> 
> QMMM                     = yes
> 
> QMMM-grps                = QMatoms
> 
> QMMMscheme               = normal
> 
> QMmethod                 = MP2
> 
> QMbasis                  = 3-21g
> 
> QMcharge                 = 0
> 
> QMmult                   = 1
> 
> The *.ORCAINFO is:
> 
> ! RKS b3lyp/g sv(p) tightscf
> 
> And I also tried QMMMsheme=ONIOM, but I get the segmentation fault
> too. Am I missing something in all of this?
> or the orca/gromcas can not be used  to non periodic system?
> Any help would be highly appreciated.
> 
> Thanks
> 
> Yan
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