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

[Mark Abraham]

Hi,

Avoiding these kind of artefacts is exactly why the recommended procedure
is to follow
http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy

Mark

On Tue, Mar 28, 2017 at 2:02 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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 <018-471%2045%2039>
> > 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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