Dear GROMACS Users:
As I mentioned, I got the following log file when I used the mdrun
command. I installed GROMACS on my virtual machine. Is there any solution
to this problem?
Thanks!
Andy
PLEASE READ AND CITE THE FOLLOWING REFERENCE
H. J. C. Berendsen, D. van der Spoel and R. van Drunen
GROMACS: A message-passing parallel molecular dynamics implementation
Comp. Phys. Comm. 91 (1995) pp. 43-56
--- Thank You ---
Changing rlist from 1.05 to 1 for non-bonded 4x4 atom kernels
Input Parameters:
integrator = steep
nsteps = 200
init-step= 0
cutoff-scheme= Verlet
ns_type = Grid
nstlist = 10
ndelta = 2
nstcomm = 100
comm-mode= Linear
nstlog = 1000
nstxout = 0
nstvout = 0
nstfout = 0
nstcalcenergy= 100
nstenergy= 1000
nstxtcout= 0
init-t = 0
delta-t = 0.001
xtcprec = 1000
fourierspacing = 0.12
nkx = 48
nky = 48
nkz = 48
pme-order= 4
ewald-rtol = 1e-05
ewald-geometry = 0
epsilon-surface = 0
optimize-fft = FALSE
ePBC = xyz
bPeriodicMols= FALSE
bContinuation= FALSE
bShakeSOR= FALSE
etc = No
bPrintNHChains = FALSE
nsttcouple = -1
epc = No
epctype = Isotropic
nstpcouple = -1
tau-p= 1
ref-p (3x3):
ref-p[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
ref-p[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
ref-p[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress (3x3):
compress[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
refcoord-scaling = No
posres-com (3):
posres-com[0]= 0.0e+00
posres-com[1]= 0.0e+00
posres-com[2]= 0.0e+00
posres-comB (3):
posres-comB[0]= 0.0e+00
posres-comB[1]= 0.0e+00
posres-comB[2]= 0.0e+00
verlet-buffer-drift = 0.005
rlist= 1
rlistlong= 1
nstcalclr= 10
rtpi = 0.05
coulombtype = PME
coulomb-modifier = Potential-shift
rcoulomb-switch = 0
rcoulomb = 1
vdwtype = Cut-off
vdw-modifier = Potential-shift
rvdw-switch = 0
rvdw = 1
epsilon-r= 1
epsilon-rf = inf
tabext = 1
implicit-solvent = No
gb-algorithm = Still
gb-epsilon-solvent = 80
nstgbradii = 1
rgbradii = 1
gb-saltconc = 0
gb-obc-alpha = 1
gb-obc-beta = 0.8
gb-obc-gamma = 4.85
gb-dielectric-offset = 0.009
sa-algorithm = Ace-approximation
sa-surface-tension = 2.05016
DispCorr = No
bSimTemp = FALSE
free-energy = no
nwall= 0
wall-type= 9-3
wall-atomtype[0] = -1
wall-atomtype[1] = -1
wall-density[0] = 0
wall-density[1] = 0
wall-ewald-zfac = 3
pull = no
rotation = FALSE
disre= No
disre-weighting = Conservative
disre-mixed = FALSE
dr-fc= 1000
dr-tau = 0
nstdisreout = 100
orires-fc= 0
orires-tau = 0
nstorireout = 100
dihre-fc = 0
em-stepsize = 0.01
em-tol = 10
niter= 20
fc-stepsize = 0
nstcgsteep = 1000
nbfgscorr= 10
ConstAlg = Lincs
shake-tol= 0.0001
lincs-order = 4
lincs-warnangle = 30
lincs-iter = 1
bd-fric = 0
ld-seed = 1993
cos-accel= 0
deform (3x3):
deform[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
deform[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
deform[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
adress = FALSE
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1= 0
userreal2= 0
userreal3= 0
userreal4= 0
grpopts:
nrdf: 22677
ref-t: 0
tau-t: 0
anneal: No
ann-npoints: 0
acc: 0 0 0
nfreeze: N
