[gmx-users] qm-mm calculation

[Justin Lemkul]

On 7/14/13 11:36 AM, Nilesh Dhumal wrote:
> Hello,
> I am trying to run the qm-mm gas phase calculations for my system.
>
>   I am using following in md.mdp file.
>
> title               =  cpeptide MD
> cpp                 =  /usr/bin/cpp
> integrator          =  md
> dt                  =  0.001    ; ps !
> nsteps              =  5000000     ; total 5 ps.
> nstcomm             =  1
> nstxout             =  1
> nstvout             =  1
> nstfout             =  1
> nstlist             =  1
> ns_type             = simple
> rlist               =  0.0
> rcoulomb            =  0.0
> rvdw                =  0.0
> coulombtype         = cut-off
> vdwtype             = cut-off
> pbc                 = no
> fourierspacing      = 0.12
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> pme_order           = 4
> ewald_rtol          = 1e-5
> optimize_fft        = yes
> ; Berendsen temperature coupling is on
> Tcoupl = nose-hoover
> tau_t = 0.1
> tc-grps  =system
> ref_t =   350
> ; Pressure coupling is  on
> Pcoupl              = no ;Parrinello-Rahman
> pcoupltype          = isotropic
> tau_p               =  2.0
> compressibility     =  4.5e-5
> ref_p               =  1.0
> ; Generate velocites is on at 300 K.
> gen_vel             =  yes
> gen_temp            =  350.0
> gen_seed            =  173529
> QMMM                     = yes
> QMMM-grps                = System
> QMmethod                 = RHF
> QMbasis                  = 3-21G
> QMcharge                 = 0
> QMmult                   = 1
>
>
> I could run the grompp and for mdrun I am getting following error.
>
> Back Off! I just backed up md.log to ./#md.log.2#
> Reading file 1.tpr, VERSION 4.0.7 (single precision)
> QM/MM calculation requested.
> there we go!
> Layer 0
> nr of QM atoms 32
> QMlevel: RHF/3-21G
>
> number of CPUs for gaussian = 1
> memory for gaussian = 50000000
> accuracy in l510 = 8
> NOT using cp-mcscf in l1003
> Level of SA at start = 0
> [c63:25888] *** Process received signal ***
> [c63:25888] Signal: Segmentation fault (11)
> [c63:25888] Signal code: Address not mapped (1)
> [c63:25888] Failing at address: (nil)
> [c63:25888] [ 0] /lib64/libpthread.so.0 [0x2b2d89ac1a90]
> [c63:25888] [ 1] /lib64/libc.so.6(strlen+0x40) [0x2b2d89d4b590]
> [c63:25888] [ 2] /lib64/libc.so.6(fputs+0x1e) [0x2b2d89d33dde]
> [c63:25888] [ 3] mdrun(init_gaussian+0x4c3) [0x51e993]
> [c63:25888] [ 4] mdrun(init_QMMMrec+0xef8) [0x517578]
> [c63:25888] [ 5] mdrun(mdrunner+0x1019) [0x42e109]
> [c63:25888] [ 6] mdrun(main+0x3c5) [0x434b95]
> [c63:25888] [ 7] /lib64/libc.so.6(__libc_start_main+0xe6) [0x2b2d89ced586]
> [c63:25888] [ 8] mdrun [0x415cb9]
> [c63:25888] *** End of error message ***
> Segmentation fault
>
> Could you tell what is the problem.
>

Debugging code that is nearly 4 years old is not very productive for the 
development team.  If you can reproduce the problem with version 4.6.3, it's 
more likely to get attention, as countless changes, enhancements, and 
improvements have taken place in the intervening time, any of which may have 
implications for whatever it is that you're trying to do.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Associate

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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