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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==================================================
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