[AMBER] namd and amber md energies do not match

From: Akshay Prabhakant <akshayresearch16.gmail.com>
Date: Fri, 12 Apr 2019 00:03:01 +0530

I have performed single step minimization, on a solvated, counter-ionised
apo-CAP system, ensuring all of the parameters I could check to be the same
in amber-md and namd, but the vanderwaal and electrostatic interaction
energy values for both of the softwares seems to be different.
1. What could be the possible reason(s) behind this?
2. How can I adjust the parameters pertaining to both the softwares, such
that I get equal values of all the properties for my system.

###### AMBER MD OUTPUT #######
efault_name


General flags:
     imin = 1, nmropt = 0

Nature and format of input:
     ntx = 1, irest = 0, ntrx = 1

Nature and format of output:
     ntxo = 2, ntpr = 1, ntrx = 1, ntwr =
   1
     iwrap = 0, ntwx = 0, ntwv = 0, ntwe =
   0
     ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat=
  0

Potential function:
     ntf = 1, ntb = 1, igb = 0, nsnb =
  25
     ipol = 0, gbsa = 0, iesp = 0
     dielc = 1.00000, cut = 30.00000, intdiel = 1.00000

Frozen or restrained atoms:
     ibelly = 0, ntr = 0

Energy minimization:
     maxcyc = 2, ncyc = 1, ntmin = 1
     dx0 = 0.01000, drms = 0.00010

Ewald parameters:
     verbose = 0, ew_type = 0, nbflag = 1, use_pme =
   1
     vdwmeth = 1, eedmeth = 1, netfrc = 0
     Box X = 100.667 Box Y = 80.729 Box Z = 65.030
     Alpha = 90.000 Beta = 90.000 Gamma = 90.000
     NFFT1 = 100 NFFT2 = 80 NFFT3 = 72
     Cutoff= 30.000 Tol =0.100E-04
     Ewald Coefficient = 0.08521
     Interpolation order = 4

--------------------------------------------------------------------------------
   3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------

default_name

 begin time read from input coords = 0.000 ps

 Number of triangulated 3-point waters found: 11634

     Sum of charges from parm topology file = -0.00000027
     Forcing neutrality...

--------------------------------------------------------------------------------
   4. RESULTS
--------------------------------------------------------------------------------

 ---------------------------------------------------
 APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
 using 5000.0 points per unit in tabled values
 TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
| CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
| CHECK d/dx switch(x): max rel err = 0.7285E-11 at 2.543240
 ---------------------------------------------------
| Local SIZE OF NONBOND LIST = 225312253
| TOTAL SIZE OF NONBOND LIST = 225312253


   NSTEP ENERGY RMS GMAX NAME NUMBER
      1 -9.2916E+04 9.4080E+01 1.6147E+04 HD13 2987

 BOND = 321.4453 ANGLE = 1117.2120 DIHED =
 5411.5371
 VDWAALS = 19766.2041 EEL = -140152.5568 HBOND =
0.0000
 1-4 VDW = 2589.8056 1-4 EEL = 18030.1890 RESTRAINT =
0.0000



####### NAMD OUTPUT #######
TCL: Minimizing for 2 steps
PRESSURE: 0 17173.6 -424.016 1589.13 -424.016 18023.3 -200.171 1589.13
-200.171 21953
GPRESSURE: 0 17173.6 -424.016 1589.13 -424.016 18023.3 -200.171 1589.13
-200.171 21953
ETITLE: TS BOND ANGLE DIHED
IMPRP ELECT VDW BOUNDARY MISC
  KINETIC TOTAL TEMP POTENTIAL TOTAL3
      TEMPAVG PRESSURE GPRESSURE VOLUME
 PRESSAVG GPRESSAVG

ENERGY: 0 321.4454 1117.2122 5411.5377
 0.0000 -118524.1228 22267.0966 0.0000 0.0000
     0.0000 -89406.8308 0.0000 -89406.8308
-89406.8308 0.0000 19049.9796 19049.9796
528476.3651 19049.9796 19049.9796

OPENING EXTENDED SYSTEM TRAJECTORY FILE
LDB: ============= START OF LOAD BALANCING ============== 25.8705
LDB: ============== END OF LOAD BALANCING =============== 25.8706
Info: useSync: 0 useProxySync: 0
LDB: =============== DONE WITH MIGRATION ================ 25.8711
MINIMIZER SLOWLY MOVING 6 ATOMS WITH BAD CONTACTS DOWNHILL
PRESSURE: 1 16856.4 -667.709 1279.15 -667.709 17799 -146.969 1279.15
-146.969 18043.8
GPRESSURE: 1 16856.4 -667.709 1279.15 -667.709 17799 -146.969 1279.15
-146.969 18043.8
ENERGY: 1 338.6619 1117.5121 5411.4505
 0.0000 -118524.6212 19423.8349 0.0000 0.0000
     0.0000 -92233.1619 0.0000 -92233.1619
-92233.1619 0.0000 17566.3788 17566.3788
528476.3651 17566.3788 17566.3788

WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 1
MINIMIZER STARTING CONJUGATE GRADIENT ALGORITHM
LINE MINIMIZER REDUCING GRADIENT FROM 9.29104e+07 TO 92910.4
OPENING COORDINATE DCD FILE
WRITING COORDINATES TO DCD FILE temp_min_1.dcd AT STEP 1
WRITING COORDINATES TO RESTART FILE AT STEP 1
FINISHED WRITING RESTART COORDINATES
The last position output (seq=1) takes 0.002 seconds, 812.500 MB of memory
in use
WRITING VELOCITIES TO RESTART FILE AT STEP 1
FINISHED WRITING RESTART VELOCITIES



#### NAMD INPUT PARAMETERS ######
## OUTPUT/INPUT
# Amber/(t,s,x)leap generated parm and crd file
parmfile apo_cap.prmtop


# Input
ambercoor apo_cap.rst7
set temperature 0

# Output
restartfreq 1
dcdfreq 1
xstFreq 1
outputEnergies 1
outputPressure 1
outputname temp_min_1

## SIMULATION PARAMETERS
# AMBER FF settings
temperature $temperature
amber on
rigidBonds none
useSettle on
rigidTolerance 1.0e-8
cutoff 30.0
pairlistdist 32.0
switching on
switchdist 28.0
#exclude scaled1-4
exclude none
readexclusions yes
1-4scaling 0.833333333
scnb 2.0
zeromomentum on
ljcorrection on
watermodel tip3

# Integrator Parameters
timestep 1.00
nonbondedFreq 1
fullElectFrequency 1
stepspercycle 1

# PME settings
PME on
PMETolerance 1.0e-6
PMEInterpOrder 4
FFTWUseWisdom no
PMEGridSizeX 100
PMEGridSizeY 80
PMEGridSizeZ 72

# periodic cell
cellBasisVector1 100.6666450 0.0 0.0
cellBasisVector2 0.0 80.7289330 0.0
cellBasisVector3 0.0 0.0 65.0295520
cellOrigin 0.0 0.0 0.0

## EXECUTION SCRIPT

minimize 2
reinitvels 300.0
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Received on Thu Apr 11 2019 - 12:00:03 PDT
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