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.
Brian
On Wed, Mar 18, 2015 at 10:36 AM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Wed, Mar 18, 2015 at 11:27 AM, Brian Radak <brian.radak.accts.gmail.com
> >
> wrote:
>
> > Oh that worked great! I had heard tell of the "chamber" command in parmed
> > but could not find it in the documentation (bc I only have the Amber14
> > release manual duh).
> >
> > Semi-related follow-up: If I want to compare energies between NAMD and
> > AMBER, do I need any special flags in mdin? Is 1-4 scaling automagically
> > switched to CHARMM values?
> >
>
> You're trying to compare Amber with chamber prmtop to NAMD with CHARMM
> psf, correct? Because NAMD won't know what to do with a CHAMBER topology
> file.
>
> In that case, I would suggest starting from George's Amber-in-NAMD guide
>
> All the best,
> Jason
>
> --
> 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 - 09:00:05 PDT
