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
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Received on Fri Aug 30 2013 - 15:00:02 PDT
