Package: cp2k Version: 2.2.426-1 Severity: normal Tags: upstream,patch A bug has been found in the AMBER force field topology input regarding torsion energies. It has been fixed in upstream revision 12867.
Michael On Thu, May 02, 2013 at 11:18:03AM +0200, Teodoro Laino wrote: > Thanks Letif and apologies for the delay. > > The issue was indeed a bug and the fix is in the SVN. Should you > encounter other discrepancies, please, do not hesitate to report them. > best, > > Teo > > On Apr 22, 2013, at 8:54 PM, Letif Mones <[email protected]> wrote: > > > Hi Teo, > > > > I am sending the following files: amber and cp2k inputs, amber > > restart file and amber topology file (dmpoh_vacuum.atop). I also > > attached another topology file (dmpoh_vacuum_mod.atop) in which I > > halved the dihedral force constants. With this latter cp2k gives the > > right answer. > > > > Regards, > > > > Letif > > > > > > > > > > On 22 Apr 2013, at 17:53, Teodoro Laino wrote: > > > >> Dear Letif, > >> > >> thanks for reporting this issue. All parameters should be converted > >> at the moment they are read. We also had few examples to check the > >> numerics and I remember they were matching with Sander they were > >> OK. Do you have an input file (including all relevant files) that > >> shows this problem? > >> > >> Thanks, > >> Teo > >> > >> On Apr 22, 2013, at 5:23 PM, Letif Mones <[email protected]> wrote: > >> > >>> Hi, > >>> > >>> I did a molecular mechanical calculation in cp2k using an amber > >>> topology file (force field: amber99). When I checked the bonded > >>> energy terms I found that the bond and angle terms are correct but > >>> the dihedral energy is twice as the energy calculated by sander. I > >>> think the reason is that in the amber FF the form of the torsion > >>> potential is: K / 2 * [ 1 + cos[ M*PHI - PHI0 ] ] while cp2k uses > >>> the form of K * [ 1 + cos[ M*PHI - PHI0 ] ]. So should not the > >>> torsion force constant read from an amber topology file be > >>> multiplied by 0.5 (and the improper one too as it has the same > >>> form)? > >>> > >>> Letif -- To UNSUBSCRIBE, email to [email protected] with a subject of "unsubscribe". Trouble? Contact [email protected]
