Ah yes, I forgot to turn on RATTLE in NAMD. I had already set ntf = 2 in
AMBER. Even so, the energies are a bit different:
NAMD w/RATTLE "all": BOND = 277.4616
AMBER (ntf=2) : BOND = 272.9150
By mdin is *very* minimal:
&cntrl
nstlim=0, igb=6, ntf=2
/
Anything else?
On Wed, Mar 18, 2015 at 11:03 AM, Jason Swails <jason.swails.gmail.com>
wrote:
> 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
>
--
Brian Radak
Postdoctoral Scholar
University of Chicago
Department of Biochemistry & Molecular Biology
Gordon Center for Integrative Science, W323A
929 E. 57th St.
Chicago, IL 60637-1454
Tel: 773/834-2812
e-mail: radak.uchicago.edu
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Received on Wed Mar 18 2015 - 09:30:03 PDT
