AMBER Archive (2003)

Subject: 10-12 H-bond terms

From: Ioana Cozmuta (ioana_at_nas.nasa.gov)
Date: Fri May 09 2003 - 17:27:53 CDT

Hi,

I did run NPT dynamics in amber for a box of water and afterwards I wanted
to compare the results with the energies calculated in NAMD (I started
the NAMD with the restart file generated in amber).
I used SHAKE thus the bond energy should be zero (which it is in amber).
However in NAMD this energy (although I use the same condition rigidBonds
all) is non zero. The only thing that draw my attention was a Warning in
the NAMD output file
Warning: Encounter 10-12 H-bond term
Warning: Found 216 H-H bonds.
In amber the EHBOND term is zero. But I am not sure what happens in NAMD,
how does it treat the H-bond interactions. In principle by turning on
amber in NAMD I would expect NAMD to treat the H-bonded interactions the
same way amber does.

Could anyone please help me understand how this works?

Thank you,
Ioana

Here is my amber input file:
Heating up the system
 &cntrl
  imin = 0, irest = 1, ntx = 5,
  ntt = 1, temp0 = 300.0, tautp = 0.2,
  vlimit = 20.0,
  ntp = 1, taup = 0.2, pres0 = 1.0, comp = 44.6, npscal = 1,
  ntb = 2, ntc = 2, ntf = 2, iwrap = 1,
  cut = 6.5, scnb = 2.0, scee = 1.2,
  nstlim = 50000, nscm = 0, t = 0.0, dt = 0.001,
  ntwe = 500, ntwx = 500, ntpr = 100, ntwr = 500,
 &end

My NAMD configuration file:
#Configuration file for NAMD, NVT run trying to heat up a water box
#from 0K to 300K

# initial config
amber on
parmfile ./spcWatBoxNpt.prmtop
coordinates ./npt.pdb
temperature 300
seed 314159

exclude scaled1-4
1-4scaling 0.8333 #=1/1.2 from Amber
scnb 2.0 #this is for the van der waals

restartfreq 100
outputEnergies 1
outputTiming 500
xstFreq 500
dcdFreq 100
outputname SPC_namdAmb
restartname SPC_namdAmb.restrt
binaryrestart no
binaryoutput no
DCDfile SPC_namdAmb.dcd
COMmotion no
wrapAll on
wrapNearest on

switching on
switchdist 6.0
cutoff 6.5
pairlistdist 8.0

#Amber uses rigid water and SHAKE H-bonds.
rigidBonds water

timestep 1
nonBondedFreq 1
fullElectFrequency 1
stepsPerCycle 1

#constant pressure simulation
berendsenPressure on
berendsenPressureTarget 1.01325
berendsenPressureCompressibility 44.6e-6
berendsenPressureRelaxationTime 200
berendsenPressureFreq 1

# periodic cell
cellBasisVector1 18.5908 00.00 00.00
cellBasisVector2 00.00 18.3002 00.00
cellBasisVector3 00.00 00.00 18.6868
cellOrigin 9.295 9.150 9.343

# full electrostatics
Pme on
PmeGridSizeX 32
PmeGridSizeY 32
PmeGridSizeZ 32

#pressure control with SHAKE
useGroupPressure yes
useFlexibleCell yes
useConstantRatio yes

# protocol params
numsteps 50

Last step energies from amber:

 NSTEP = 50000 TIME(PS) = 75.000 TEMP(K) = 293.29 PRESS = -946.0
 Etot = -2045.2216 EKtot = 377.6677 EPtot = -2422.8893
 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 423.1656
 EELEC = -2846.0549 EHBOND = 0.0000 RESTRAINT = 0.0000
 EKCMT = 193.4049 VIRIAL = 323.2904 VOLUME = 6358.8682
                                                Density = 1.0162
 Ewald error estimate: 0.9242E-03

First step energies in NAMD ETITLE:
TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP
PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG ENERGY:
0 0.0157 0.0000 0.0000 0.0000 -2847.2957 462.0643 0.0000 0.0000 428.0760
-1957.1397 285.5104 30670.2959 -622.3834 6357.5364 30670.2959 -622.3834