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

Justin Lemkul jalemkul at vt.edu
Tue Mar 28 14:00:55 CEST 2017

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On 3/28/17 4:26 AM, Erik Marklund wrote:
> Dear Yvon,
>
> Are you sure you ‘re not constraining, say, H-bonds in one and not the other?
>

This is almost certainly the case.  We've done extensive validation of CHARMM
vs. GROMACS energies and the agreement is nearly perfect if calculated properly.

-Justin

> 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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--
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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