lin hen wrote:
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
#nsteps = -1
nsteps = 100
nstlist = 0
ns_type = grid
rlist = 0
coulombtype = cut-off
vdwtype = cut-off
rcoulomb = 0
rvdw = 0
pbc = no
epsilon_rf = 0
rgbradii = 0
comm_mode = angular
implicit_solvent = GBSA
gb_algorithm = OBC
gb_epsilon_solvent = 78.3
sa_surface_tension = 2.25936
nstxout = 0
nstfout = 0
nstvout = 0
nstxtcout = 0
nstlog = 0
nstcalcenergy = -1
nstenergy = 0
tcoupl = berendsen
tc-grps = system
tau-t = 0.1
ref-t = 300
This is the .mdf file, even I modified the nsteps, it still comes with
the same error:
Back Off! I just backed up ener.edr to ./#ener.edr.1#
WARNING: OpenMM does not support leap-frog, will use velocity-verlet
integrator.
WARNING: OpenMM supports only Andersen thermostat with the
md/md-vv/md-vv-avek integrators.
WARNING: OpenMM provides contraints as a combination of SHAKE, SETTLE
and CCMA. Accuracy is based on the SHAKE tolerance set by the
"shake_tol" option.
WARNING: The OBC scale factors alpha, beta and gamma are hardcoded in
OpenMM with the default Gromacs values.
Pre-simulation ~15s memtest in progress...done, no errors detected
starting mdrun 'Protein'
-1 steps, infinite ps.
the log file:
Input Parameters:
integrator = md
nsteps = -1
init_step = 0
ns_type = Grid
nstlist = 0
ndelta = 2
nstcomm = 10
comm_mode = Angular
nstlog = 0
nstxout = 0
nstvout = 0
nstfout = 0
nstcalcenergy = 10
nstenergy = 0
the nsteps is still -1, did I do something wrong?
You haven't properly commented out the "nsteps = -1" line. The comment sign is
a ';' not '#' though I'm surprised grompp didn't simply abort with this input file.
-Justin
Thanks a lot
YY
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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