[gmx-users] Bond energy difference between CHARMM and GROMACS

[Erik Marklund]

Dear Yvon,

Are you sure you ‘re not constraining, say, H-bonds in one and not the other?

Kind regards,
Erik
______________________________________________
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.marklund at kemi.uu.se<mailto:erik.marklund at kemi.uu.se>

On 28 Mar 2017, at 07:55, Yvon Wong <wong.yvon at gmail.com<mailto:wong.yvon at gmail.com>> wrote:

I try to compare the energy in CHARMM and GROMACS.
After running 4 systems I found the dihedral energies are the same, but the
bond energies are different.
Can somebody help me to solve this problem?

(1)Only one residue: MET

Bond:

0.44*4.18   =   1.839 (CHARMM)  ====>  2.587 (GROMACS)   (different)
Dihedral:

3.687* 4.18 = 15.4116 (CHRAMM)  ====> 15.4448 (GROMACS)  (the same)

(2)Only one residue: GLY
BONDS:

 0.34243*4.18=  1.431  ===> 1.209


Dihedrals
1.77911*4.18 = 7.436  ===> 7.447

(3)5 -residue:  ASN GLY PHE TRP THR
BONS:

4.82777* 4.18=    20.1800   ====>   22.58


DIHE:
37.82747*4.18 =  158.1188   ====>  158.504

(4)20- residue:  GLY LYS MET PHE SER TRP TYR VAL ALA ARG CYS VAL PRO
TRP MET SER SER LYS LYS MET
BONDS

17.48049 * 4.18 =    73.068  =======>   78.64


DIHE

185.71    * 4.18  =   776.26  =======>  777.32
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