[gmx-users] Gromacs DFTB problem
Gábor Balogh
gaborbalogh91 at gmail.com
Fri Mar 4 10:56:54 CET 2016
Dear Gromacs users,
I have compiled a DFTB implementation for GROMACS:
http://cbp.cfn.kit.edu/joomla/index.php/downloads/18-gromacs-with-qm-mm-using-dftb3
The system consists of the catalytic domain of a protein in explicit
solvent (TIP3P). Long-range electrostatics is calculated using the PME
scheme. Conjugate-gradient energy minimization runs fine, but NVT
equilibration terminates after 16-44 ps (depending on PME options and
velocity generation) with the following error message:
DSYGVD: ier = 214
EXITING!
MD options:
define = -DPOSRES_SIM
;
integrator = md
; 1 ns
nsteps = 1000000
dt = 0.001
; Output control
nstxout = 20000
nstvout = 20000
nstenergy = 10000
nstlog = 2000
nstxtcout = 10000
xtc-grps = Protein
;
continuation = no
constraint_algorithm = lincs
constraints = all-bonds
;
ns_type = grid
nstlist = 10
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.0
;
coulombtype = PME
pme_order = 4
fourierspacing = 0.12
;
tcoupl = V-rescale
tc-grps = Protein_Link Water_and_ions
tau_t = 0.1 0.1
ref_t = 310 310
;
pcoupl = no
; Periodic boundary conditions
pbc = xyz
;
DispCorr = EnerPres
;
gen_vel = yes
gen_temp = 310
gen_seed = -1
;
cutoff-scheme = group
; dftb
QMMM = yes
QMMM-grps = QMsystem ; needs to be specified in the index file
QMMMscheme = normal
QMmethod = RHF ; required but ignored
QMbasis = STO-3G ; required but ignored
QMcharge = -1 ; an integer
MMchargescalefactor = 1. ; or smaller
; DFTB
QMdftbsccmode = 3 ; for DFTB3, or 2 for DFTB2 (a.k.a. SCC-DFTB)
QMdftb-telec = 310. ; "electronic temperature" for the Fermi
distribution
QMdftb-slko-path = /scratch1/BG/gro/slko_gmx/ ; path to the
parameter files including the trailing slash
QMdftb-slko-separator = ; possibly the character between element
names
QMdftb-slko-lowercase = yes ; or no, in the file names ("Ca"
vs. "ca")
QMdftb-slko-suffix = -c.spl ; of the file names
QMdftb-partial-pme = 0 ; accelerated PME calculations -
recommended (0 to switch off)
QMdftb-dispersion = 0 ; for D3, or 0 for no dispersion
QMdftb-cdko = 0 ; currently not implemented
QMdftb-mmhub-inf = 1 ; currently not implemented
Last lines of Gromacs-DFTB output:
STEP 24856
The number of MM atoms is 15355
MM+ETC TIME: 24791883
EWALD-SR START
DFTB SR TIME: 1860179
EWALD-SR END
DFTB PRE TIME: 2965810
SCC ITER TIME: 68803390
DFTB PME TIME: 4833495
DFTB DIA TIME: 12378935
SCC ITER TIME: 20096442
DFTB PME TIME: 4796196
DFTB DIA TIME: 12375332
SCC ITER TIME: 20050119
DFTB PME TIME: 4764749
DFTB DIA TIME: 12401352
SCC ITER TIME: 20061356
DFTB PME TIME: 4765373
DFTB DIA TIME: 7992655
DSYGVD: ier = 214
EXITING!
Could somebody help me to find out why the simulation is crashing?
Thanks in advance.
Best regards,
Gabor
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