From: Yi Shang (mirandaisbest_at_gmail.com)
Date: Mon Jul 20 2009 - 18:31:47 CDT
Hi all,
I did some comparison of energy calculated by NAMD 2.7b1 and AMBER 10. I
found something intriguing.
During simulation, VDW energy from AMBER simulation is constantly much lower
from NAMD. So I tried to compare point energy first. I turned off SHAKE,
temperature, and pressure control and only looked at basic energy
calculation of one single structure: bonds, angles, dihedrals,
electrostatic, and vdw energies.
For non-periodic boundary, I had no problem, energies are exactly the same.
For periodic boundary condition here comes the problem:
-electro energy off by ~14kcal/mol, which is ok, parameters might not be
identical in two methods.
-vdw energy off by > 600 kcal/mol. That's terrible.
I tested these inputs on two different periodic systems, and I get the same
result (same energy gap). So I don't think it's system specific problem.
Here is my inputs and outputs from one system's comparison (I combined AMBER
VDWAALS and 1-4 NB energies to compare to NAMD vdw energy, likewise for
electrostatic interaction):
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
NAMD config.in:
amber on
parmfile box.top
ambercoor box.crd
binaryoutput no
outputname md6
outputpressure 1
outputenergies 1
exclude scaled1-4
1-4scaling 0.83333
timestep 2
temperature 0
cutoff 8
switching off
PME yes
PMEGridSpacing 1.0
cellbasisvector1 79.6614 0 0
cellbasisvector2 0 60.2065 0
cellbasisvector3 0 0 63.7403
cellorigin 0 0 0
run 0
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
amber md.in:
&cntrl
imin = 0, nstlim = 1, dt = 0.002,
irest = 0, ntx = 1,
tempi = 0.0, temp0 = 0.0,
ntwx = 0, ntwe = 0, ntwr = 0, ntpr = 1,
cut = 8.0,
/
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
namd energies:
ETITLE: TS BOND ANGLE DIHED
IMPRP ELECT VDW BOUNDARY MISC
KINETIC TOTAL TEMP POTENTIAL
TOTAL3 TEMPAVG PRESSURE GPRESSURE VOL
UME PRESSAVG GPRESSAVG
ENERGY: 0 341.5078 716.0018 2372.7673
0.0000 -67739.0356 7208.9795 0.0000 0.0000
0.0000 -57099.7791 0.0000 -57099.7791
-56529.2524 0.0000 11740.3005 -276.1608 305707.0
250 11740.3005 -276.1608
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
amber energies:
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
0.0
Etot = -57686.8091 EKtot = 0.0000 EPtot =
-57686.8091
BOND = 341.5077 ANGLE = 716.0017 DIHED =
2372.7669
1-4 NB = 1076.3715 1-4 EEL = 9100.8801 VDWAALS =
5527.3094
EELEC = -76821.6464 EHBOND = 0.0000 RESTRAINT =
0.0000
Ewald error estimate: 0.2976E-03
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
It's strange because in NAMD seems most important parameter I would play
around with VDW energy is switching, and it's turned off. Same cutoff is set
in two inputs, but still, I get very different results.
any suggestions would be appreciated! Thanks!
-- Miranda
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