On Wed, 2015-03-18 at 10:54 -0500, Brian Radak wrote:
> Here is the output from NAMD with the input PSF/PDB and from AMBER with the
> output PARM7/RST7. This is just a dipeptide in vacuum with 999. cutoff and
> no switching/shifting. The potential energies are in bold.
>
> ETITLE: TS BOND ANGLE DIHED IMPRP
> ELECT VDW BOUNDARY MISC
> KINETIC
> TOTAL TEMP POTENTIAL TOTAL3
> TEMPAVG
> ENERGY: 0 296.7573 68.9638 10.7652
> 0.8898
> -82.0083 296.9008 0.0000 0.0000
> 0.0000
> 592.2686 0.0000 *592.2686* 602.4975
> 0.0000
>
>
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS
> = 0.0
> Etot = 568.4243 EKtot = 0.0000 EPtot
> = *568.4243*
> BOND = 272.9150 ANGLE = 42.2312 DIHED =
> 10.5283
> UB = 26.7326 IMP = 0.8898 CMAP
> = 0.2369
> 1-4 NB = 181.3726 1-4 EEL = 32.7326 VDWAALS =
> 115.5281
> EELEC = -114.7428 EGB = 0.0000 RESTRAINT =
> 0.0000
>
> Upon closer inspection the following make sense:
>
> NAMD TERMS : AMBER TERMS
> -------------------------------------------------
> ELECT = 1-4EEL + EELEC
> -82.0083 ~= 32.7326 -114.7428 = -82.0102
>
> VDW = 1-4 NB + VDWAALS
> 296.9008 ~= 181.3726 + 115.5281 = 296.9007
>
> ANGLE = ANGLE + UB
> 68.9638 = 42.2312 + 26.7326 = 68.9638
>
> DIHED = DIHED + CMAP
> 10.7652 = 10.5283 + 0.2369 = 10.7652
>
> IMPRP = IMP
> 0.8898 = 0.8898
>
> But the bonded energies don't match:
> 296.7573 != 272.9150
>
> I'm not really sure what to do with that.
Is ntf=2?
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Mar 18 2015 - 09:30:02 PDT
