Dear AMBER Community,
I am trying to reproduce the results of “Analysis of a nucleic acid simulation” tutorial.[1]
I am facing a problem while running “eq.in” script as it's throwing an error[2] even before 1st step.
I am using Amber 20 PMEMD 2020 on CPUs. All the scripts before this step i.e. mini.in & heat.in, are running fine.
Can somebody please point-out where I am getting it wrong.
Thank you.
[1]
https://amberhub.chpc.utah.edu/analisis-of-nucleic-acid-simulation/ <
https://amberhub.chpc.utah.edu/analisis-of-nucleic-acid-simulation/>
[2]
Nature and format of output:
ntxo = 2, ntpr = 500, ntrx = 1, ntwr = 500
iwrap = 0, ntwx = 500, ntwv = 0, ntwe = 500
ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat= 0
Potential function:
ntf = 2, ntb = 2, igb = 0, nsnb = 25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 9.00000, intdiel = 1.00000
Frozen or restrained atoms:
ibelly = 0, ntr = 1
restraint_wt = 0.50000
Molecular dynamics:
nstlim = 25000, nscm = 0, nrespa = 1
t = 0.00000, dt = 0.00200, vlimit = 20.00000
Berendsen (weak-coupling) temperature regulation:
temp0 = 300.00000, tempi = 0.00000, tautp = 0.20000
Pressure regulation:
ntp = 1
pres0 = 1.00000, comp = 44.60000, taup = 0.20000
SHAKE:
ntc = 2, jfastw = 0
tol = 0.00001
| Intermolecular bonds treatment:
| no_intermolecular_bonds = 1
| Energy averages sample interval:
| ene_avg_sampling = 500
Extra-points options:
frameon = 1, chngmask= 1
Ewald parameters:
verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1
vdwmeth = 1, eedmeth = 1, netfrc = 1
Box X = 62.425 Box Y = 62.425 Box Z = 62.425
Alpha = 109.471 Beta = 109.471 Gamma = 109.471
NFFT1 = 64 NFFT2 = 64 NFFT3 = 64
Cutoff= 9.000 Tol =0.100E-04
Ewald Coefficient = 0.30768
Interpolation order = 4
LOADING THE CONSTRAINED ATOMS AS GROUPS
5. REFERENCE ATOM COORDINATES
default_name
Mask :1-24; matches 758 atoms
| EXTRA_PTS, trim_bonds: num bonds BEFORE trim = 15575 0
| EXTRA_PTS, trim_bonds: num bonds AFTER trim = 15575 0
| EXTRA_PTS, trim_bonds: num bonds BEFORE trim = 5645 0
| EXTRA_PTS, trim_bonds: num bonds AFTER trim = 544 0
| EXTRA_PTS, trim_theta: num angle BEFORE trim = 640 0
| EXTRA_PTS, trim_theta: num angle AFTER trim = 640 0
| EXTRA_PTS, trim_theta: num angle BEFORE trim = 836 0
| EXTRA_PTS, trim_theta: num angle AFTER trim = 836 0
| EXTRA_PTS, trim_phi: num diheds BEFORE trim = 1390 0
| EXTRA_PTS, trim_phi: num diheds AFTER trim = 1390 0
| EXTRA_PTS, trim_phi: num diheds BEFORE trim = 1756 0
| EXTRA_PTS, trim_phi: num diheds AFTER trim = 1756 0
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
default_name
begin time read from input coords = 100.000 ps
Unit 15 Error on OPEN: mden
——
Jatin Kashyap
Ph.D. Student
Dr. Dibakar Datta Group
Department of Mechanical and Industrial Engineering
New Jersey Institute of Technology (NJIT)
University Heights
Newark, NJ 07102-1982
Phone- (201)889-5783
Email- jk435.njit.edu
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Received on Mon Jan 18 2021 - 15:30:02 PST
