Re: inconsistence in NAMD and AMBER energy

From: Goutham (gouthambs_at_gmail.com)
Date: Tue Jul 21 2009 - 01:13:48 CDT

Is it possible that you are using different force parameters for the two
cases?

On Mon, Jul 20, 2009 at 4:31 PM, Yi Shang <mirandaisbest_at_gmail.com> wrote:

> 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
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:51:14 CST