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

[David van der Spoel]

The correct value for kcal conversion is 4.184, however that does not 
explain the difference. Maybe you can try to take one exampel, e.g. the 
first one and test it bond by bond (by turning on one term at a time in 
the topology). I assume this is for 0 steps of MD or EM?


Den 2017-03-28 kl. 07:55, skrev Yvon Wong:
> 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

-- 
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se