Dear Dr. Ross Walker,
Thank you for your suggestion.
I am now able to match the VDW energy between CHARMM and AMBER. For ELEC,
though the PME parameters are the same, there is some difference in energy
which is consistent with the AMBER test case of DHFR.
CHARMM:
cton=ctof=9, no shake
kappa 0.340 pmEwald order 4 fftx 108 ffty 108
fftz 108
ENER ENR: Eval# ENERgy Delta-E GRMS
ENER INTERN: BONDs ANGLes UREY-b DIHEdrals
IMPRopers
ENER CROSS: CMAPs PMF1D PMF2D PRIMO
ENER EXTERN: VDWaals ELEC HBONds ASP
USER
ENER IMAGES: IMNBvdw IMELec IMHBnd RXNField
EXTElec
ENER EWALD: EWKSum EWSElf EWEXcl EWQCor
EWUTil
---------- --------- --------- --------- ---------
---------
ENER> 0-185057.38479 30034.40797 14.18259
ENER INTERN> 5091.22704 17744.99438 5862.57551 18429.68264
312.64340
ENER CROSS> -45.81685 0.00000 0.00000 0.00000
ENER EXTERN> 7877.73384-183453.70289 0.00000 0.00000
0.00000
ENER IMAGES> -1103.32132 -11082.53004 0.00000 0.00000
0.00000
ENER EWALD> 3211.9069-1409623.2881 1361720.5107 0.0000
0.0000
AMBER
cut=9, no shake
ew_coeff=0.340,nfft1=108,nfft2=108,nfft3=108,order=4,vdwmeth=0
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
-803.1
Etot = -185048.1581 EKtot = 0.0000 EPtot =
-185048.1581
BOND = 5091.2270 ANGLE = 17744.9944 DIHED =
18431.1978
UB = 5862.5755 IMP = 312.6434 CMAP =
-45.8167
1-4 NB = 3842.7942 1-4 EEL = 28245.3711 VDWAALS =
2931.6172
EELEC = -267464.7621 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 0.0000 VIRIAL = 16101.9497 VOLUME =
928651.5199
Density =
1.0114
Summary:
VDW ELEC
CHARMM 6774.41 -239227
AMBER 6774.4114 -239219.391
Jun Feng
On Fri, Aug 30, 2013 at 6:10 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Jun,
>
>
> Charmm uses a switching function for the VDW while AMBER uses a long range
> continuum correction - which don't match obviously. Neither is more wrong
> than the other - they are both wrong. ;-)
>
> For sanity turn off any switching function in charmm and in amber set
> vdwmeth=0 in the ewald namelist and you should be able to make the VDW
> terms match. I don't recommend running with this though - better just to
> use the default of (vdwmeth=1) when running the charmm forcefield in AMBER.
>
> Note you should be able to get EELEC to match as well - you just have to
> monkey with the ewald coefficient and FFT settings to make sure they are
> exactly the same in both codes.
>
> Note AMBER and Charmm do shake in different ways as well so for a perfect
> comparison you should turn off shake in both runs.
>
> See:
>
> $AMBERHOME/test/chamber/md_engine/dhfr_cmap_pbc
>
> All the best
> Ross
>
>
> On 8/30/13 2:55 PM, "Jun Feng" <jufeng.mail.wvu.edu> wrote:
>
> >Dear CHAMBER developers:
> >I tried to compare energy in AMBER and CHARMM under PBC. My workflow is:
> >1. created psf and pdb in CHARMM with c36 FF
> >2. use CHAMBER to generate prmtop and inpcrd
> >3. run one step energy calculation in CHARMM and pmemd under PBC using
> >PME,
> >compare energy. cut=9 in AMBER, cton=ctoff=9, cutoff=12 in CHARMM
> >Result:
> >I tried several systems and VDW energy is significantly differently under
> >PBC in all cases. But VDW energy is exactly the same in vacumm without
> >PBC(in another thread).
> >I provided one output of energy calculation under PBC:
> >#CHARMM
> >ENER ENR: Eval# ENERgy Delta-E GRMS
> >ENER INTERN: BONDs ANGLes UREY-b DIHEdrals
> > IMPRopers
> >ENER CROSS: CMAPs PMF1D PMF2D PRIMO
> >ENER EXTERN: VDWaals ELEC HBONds ASP
> >USER
> >ENER IMAGES: IMNBvdw IMELec IMHBnd RXNField
> > EXTElec
> >ENER EWALD: EWKSum EWSElf EWEXcl EWQCor
> >EWUTil
> > ---------- --------- --------- --------- ---------
> > ---------
> >ENER> 0-182266.18440 27243.20758 14.18262
> >ENER INTERN> 5091.22704 17744.99438 5862.57551 18429.68264
> > 312.64340
> >ENER CROSS> -45.81685 0.00000 0.00000 0.00000
> >ENER EXTERN> 10368.05537-183453.70289 0.00000 0.00000
> > 0.00000
> >ENER IMAGES> -809.55028 -11082.53004 0.00000 0.00000
> > 0.00000
> >ENER EWALD> 3219.0147-1409623.2881 1361720.5107 0.0000
> >0.0000
> >
> >#AMBER
> >NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
> >-1222.4
> > Etot = -187850.8243 EKtot = 0.0000 EPtot =
> >-187850.8243
> > BOND = 5091.2270 ANGLE = 17744.9944 DIHED =
> >18431.1978
> > UB = 5862.5755 IMP = 312.6434 CMAP =
> >-45.8167
> > 1-4 NB = 3842.7942 1-4 EEL = 28245.3711 VDWAALS =
> >129.0351
> > EELEC = -267464.8461 EHBOND = 0.0000 RESTRAINT =
> >0.0000
> > EKCMT = 0.0000 VIRIAL = 24509.4032 VOLUME =
> > 928651.5199
> > Density =
> >1.0114
> >
> > CHARMM AMBER
> >VDW total 9558.55 3971.8293
> >ELEC total -239219 -239219.475
> >Please also note the difference in dihedrals
> >
> >I understand that VDW energy is sensitive to cutoff, but can anybody
> >explain the HUGE and significant difference in VDW energy? I am really
> >puzzled.
> >
> >Jun Feng
> >_______________________________________________
> >AMBER mailing list
> >AMBER.ambermd.org
> >http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jun Feng
Postdoc Fellow
Blake Mertz Research Group
Department of Chemistry
West Virginia University
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Received on Tue Sep 03 2013 - 11:00:02 PDT
