David,
Thanks for replying. Here is my config script for the first simulation
&cntrl
irest=0, ! no restrt
ntx=1, ! (only coordinates will be read from a formatted file.)
imin=0, ! (no minimization)
ntr=0, !
ntf=2, ! (Force evaluation,complete interaction is calculated)
ntc=2, ! (SHAKE,bonds involving hydrogen are constrained)
tol=0.0000001, ! (shake tolerance)
iwrap=1, ! coordinates written to the restart and trajectory files
will
cut=12.0, !
fswitch=10.0,!
ntt=3, ! (Langevin dynamics for temperature control)
ig=-1, ! random seed
gamma_ln=5.0, ! (collision frequency)
temp0=310.0, ! (reference temperature)
ntp=1, ! ( pressure control, isotropic (x-,y-,z-) pressure
scaling)
ntb=2, ! (constant pressure (default when ntp > 0))
taup=8.0, ! (Pressure relaxation time)
ntpr=5000, ! (print energy output interval)
ntr = 1, ! Turn on positional restraints
ntrx =1,
restraint_wt = 10000, ! 10 kcal/mol/A**2 restraint force
const
restraintmask = '.CA,C,O,N' ! Restraints on the backbone atoms only
ntwr=5000, ! (frequency to write restart file)
ntwe=0, ! (don't write energies and temperature to mden file)
ntwx=5000, ! (write coordinates to the mdcrd file)
nstlim=10000000, ! (Number of MD-steps. 90ns, total of 100ns)
dt=0.002, !
/
For restart, I just put irest=1, ntx=5,
I didn't get what you mean by "no water box". Regarding energy, it seems
the energy part is messed up from the beginning of the second simulation.
Here is the beginning of the Results section of the output
wrapping first mol.: 4021792.86338 -2114398.73928 -2432442.38417
wrapping first mol.: 4021792.86338 -2114398.73928 -2432442.38417
NSTEP = 5000 TIME(PS) = 20005.000 TEMP(K) =********* PRESS =
-7587.4
Etot = ************** EKtot = ************** EPtot =
**************
BOND = ************** ANGLE = 4951168.7892 DIHED =
23181.8601
UB = ************** IMP = 54553.9806 CMAP =
0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0273 VDWAALS =
**************
EELEC = -415360.5968 EHBOND = 0.0000 RESTRAINT =
-0.0000
EAMBER (non-restraint) = **************
EKCMT = -0.0000 VIRIAL = 314527.1725 VOLUME =
1919929.3072
Density =
1.0008
------------------------------------------------------------------------------
Thanks,
Sadegh
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Received on Tue Mar 28 2017 - 14:00:02 PDT
