Dear Amber experts,
I'm trying to estimate the vertical energy gap as defined in Figure 4 of this
<
https://pubs.acs.org/doi/10.1021/acs.chemrev.5b00298#_i25>paper.
For this, I have ensured that prmtop files for both states are identical.
Then, I've used imin=5 prmtop of 1st state to re-calculate Amber energies
at the coordinate of the 2nd state.
I'm getting the following energies for the two states.
The mdin file is also shown below. Can you please suggest to me if these
results seem meaningful? I can't see the Etot, EKtot and EPtot values in
the mdout file while using imin=5. Did I miss/missunderstand the usage of
some keywords/options in mdin file while using imin=5?
Input file for 1st state normal md is given at the bottom of the message.
Looking forward to receiving valuable suggestions from the list.
*mdin file*
single point energy calculations of 1st state coordinates using parameters
of the 2nd state
&cntrl
ntx=1, ntpr=1, ntwx=1,
imin=5, maxcyc=1, !Single-point energy calculation on each frame
ntb=0, !Non-periodic
cut=9999., !Calculate all solute-solute interactions
/
*Energies for 1st state while using normal MD:*
NSTEP = 10000 TIME(PS) = 1050.000 TEMP(K) = 299.32 PRESS =
0.0
Etot = -49685.1834 EKtot = 12894.9072 EPtot =
-62580.0906
BOND = 404.7503 ANGLE = 1270.4594 DIHED =
1749.3757
1-4 NB = 514.7171 1-4 EEL = 7140.6069 VDWAALS =
7564.3402
EELEC = -81224.3402 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
*Energies of 1st state while using 2nd state prmtop and imin=5*
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -5.6620E+04 1.3817E+01 1.2211E+02 CG 286
BOND = 401.5878 ANGLE = 1266.0832 DIHED =
1754.2166
VDWAALS = 7317.4110 EEL = -75019.9377 HBOND =
0.0000
1-4 VDW = 516.7397 1-4 EEL = 7144.3101 RESTRAINT =
0.0000
minimization completed, ENE= -.56619589E+05 RMS= 0.138167E+02
minimizing coord set # 2
Maximum number of minimization cycles reached.
Normal MD input file for 1st state:
Production Stage in Explicit Solvent
&cntrl
ntt=3, ! Temperature scaling (=3, Langevin dynamics)
gamma_ln=2.0, ! Collision frequency of the Langevin dynamics in ps-1
ntc=2, ! SHAKE constraints (=2, hydrogen bond lengths
constrained)
ntf=2, ! Force evaluation (=2, hydrogen bond interactions
omitted)
ntb=1, ! Boundaries (=1, constant volume)
cut=10.0, ! Cutoff
dt=0.002, ! The time step in picoseconds
nstlim=20000000, ! Number of MD steps to be performed
ig=-1, ! Random seed (=-1, get a number from current date and
time)
ntwr=10000, ! Restart file written every ntwr steps
ntwx=10000, ! Trajectory file written every ntwx steps
ntpr=10000, ! The mdout and mdinfo files written every ntpr steps
ioutfm=1, ! Trajectory file format (=1, Binary NetCDF)
iwrap=1, ! Translate water molecules into the original simulation
box
igb=0, ! GB model (=0, explicit solvent)
irest=1, ! Flag to restart the simulation
ntx=5, ! Initial condition (=5, coord. and veloc. read from the
inpcrd file)
/
Thank you and best regards.
--
Regards,
Dr. Vaibhav A. Dixit,
Assistant Professor,
Department of Pharmacy,
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VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
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Phone No. +91 1596 255652, Mob. No. +91-7709129400,
Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
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Received on Fri Oct 30 2020 - 10:30:02 PDT
