From owner-nwchem-users@emsl.pnl.gov Thu Apr 6 11:31:23 2006 Received: from odyssey.emsl.pnl.gov (localhost [127.0.0.1]) by odyssey.emsl.pnl.gov (8.13.6/8.13.6) with ESMTP id k36IVM06003847 for ; Thu, 6 Apr 2006 11:31:22 -0700 (PDT) Received: (from majordom@localhost) by odyssey.emsl.pnl.gov (8.13.6/8.13.6/Submit) id k36IVMEr003846 for nwchem-users-outgoing-0915; Thu, 6 Apr 2006 11:31:22 -0700 (PDT) Date: Thu, 06 Apr 2006 14:33:43 -0300 From: JunJun Liu Subject: Re: [NWCHEM] difference between AMBER package and NWChem package In-reply-to: <7674C02157839B4D83ED0F37439BD7D0028C96BC@pnlmse23.pnl.gov> To: "Palmer, Bruce J" , "Vorpagel, Erich R" , nwchem-users@emsl.pnl.gov Message-id: MIME-version: 1.0 Content-type: text/plain; format=flowed; delsp=yes; charset=utf-8 Content-transfer-encoding: 8bit DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=beta; d=gmail.com; h=received:date:to:subject:from:content-type:mime-version:references:content-transfer-encoding:message-id:in-reply-to:user-agent; b=fMzs6JDmmJ+CN2kmOCTrJuyAI2gOGX5JtKt1Ed1oItVqCmHXqbqzi3Eedd3CtbXNNz5bsmVpTCmSf+4XUR6jKssvG7sLlOuU15tFZjZcallcJ1SfsinlHePlUOFvUOL+XJvt0pZp1ifsvukGHhQ4+GtyVfdWWiRXHShikvKNi5Q= User-Agent: Opera Mail/9.00 (Linux) References: <7674C02157839B4D83ED0F37439BD7D0028C96BC@pnlmse23.pnl.gov> Sender: owner-nwchem-users@emsl.pnl.gov Precedence: bulk yes, not only just the difference in unit. But the the scale factor fo 1/2 seems also not enough:( === AMBER 96 ===== HW-OW-HW 100. 104.52 TIP3P water ================== so, K(theta)=100 kcal/mol, Theta(eq)=104.52 degree When converted to NWChem values, it should be K(theta)=100*4.184=418.400 kj/mol Theta(eq)=104.52*2*3.1415/360=1.824 radians Obviously, it's not the same as in NWChem below. Even with a factor of 1/2. Is there any mistakes in my convertion? === NWChem ======== HW -OW -HW 1.82422 8.36800E+02 =================== regards! Liu On Thu, 06 Apr 2006 13:25:48 -0300, Palmer, Bruce J wrote: > Liu, > > I think there is also a factor of 1/2 that is included in the definition > of the harmonic potentials in NWChem that is not included in Kollman's > definition. > > Bruce Palmer > > -----Original Message----- > From: owner-nwchem-developers@emsl.pnl.gov > [mailto:owner-nwchem-developers@emsl.pnl.gov] On Behalf Of Vorpagel, > Erich R > Sent: Thursday, April 06, 2006 8:53 AM > To: JunJun Liu; nwchem-users@emsl.pnl.gov > Subject: RE: [NWCHEM] difference between AMBER package and NWChem > package > > Greetings Liu, > > NWChem uses SI units, radians for angles and kJ/mol for energy. Kollman > et al., use degrees for angles and Kcal/mol for energy. > > Erich R. Vorpagel, Ph.D. Chief Scientist > Manager Computational Grand-Challenge and Pilot Projects MSCF > Visualization and User Services Group Environmental Molecular Sciences > Laboratory Pacific Northwest National Laboratory P. O. Box 999, MS: > K8-91 > 3335 Q Ave. Phone: 509-376-0751 > Richland, WA 99352 FAX: 509-376-0420 > Email: erich.vorpagel@pnl.gov > Web: http://mscf.emsl.pnl.gov/ > > > -----Original Message----- > From: owner-nwchem-users@emsl.pnl.gov > [mailto:owner-nwchem-users@emsl.pnl.gov] On Behalf Of JunJun Liu > Sent: Wednesday, April 05, 2006 5:21 PM > To: nwchem-users@emsl.pnl.gov > Subject: [NWCHEM] difference between AMBER package and NWChem package > > Dear all > > I notice the values of AMBER force field in NWChem package and AMBER8 > package are different. For example, In > $nwchem_basis_library/amber_s/amber95.par, the angel parameter for TIP3P > is: > === > HW -OW -HW 1.82422 8.36800E+02 > === > > Whileas in AMBER force field 96: parm96.dat, the corresponding parameter > is: > === > HW-OW-HW 100. 104.52 TIP3P water > === > > Can you tell me why does such difference exist and how to convert > parameters from AMBER force field? Thanks in advance! > > Regards! > > Liu -- JunJun Liu College of Chemistry Central China Normal University WuHan 430079 P.R. China