So gromacs gives an answer of 6000 kJ/mol and some other software using the same method yields 250 kJ/mol ?
On 18 August 2016 at 22:13, Ben Tam <btam...@hotmail.co.uk> wrote: > Hi Billy, > > > To be more exact, the system has been energy minimised through DFT > calculation. We want to compare that with MM force field by using the same > co-ordinate. Henceforth we don't need an average gibbs energy but one > specific frame energy calculation. > > Best regards, > > Ben > > ________________________________ > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Billy > Williams-Noonan <billy.williams-noo...@monash.edu> > Sent: 18 August 2016 13:07 > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Problem with binding energy > > Hi Ben, > > My understanding of what you've done is that you have calculated a > binding enthalpy for the water at a specific, non-biological temperature, > and not a Gibbs free energy that you would expect from experiment... > > Billy > > On 18 August 2016 at 21:34, Ben Tam <btam...@hotmail.co.uk> wrote: > > > Dear all, > > > > > > I have a problem with calculation with binding energy with using gromacs. > > My calculation is the binding of solvent onto a crystal. > > > > > > The steps I took to calculate binding energy is like this: > > > > > > 1) Energy minimised my crystal system with the solvent. > > > > > > 2) Calculated the energy of the crystal-solvent system by using gmx > energy > > - total energy is selected (this is done by using only time 0 energy step > > shown from energy.xvg) > > > > > > 3) I extract the co-ordinate of the solvent from the minimised system and > > calculate the energy by using gmx energy - total energy is selected (this > > is done by using only time step 0 energy shown from energy.xvg) > > > > > > 4)Extract the co-ordinate of the crystal from the minimised system and > > calculate the energy similar to the previous step. > > > > > > 5) Energy of the Crystalsolvent system - energy of the crystal - energy > of > > the solvent = binding energy. > > > > > > The problem I have is, after the calculation I proposed, the binding > shown > > as -6000 kJ/mol. With other software, the binding energy is calculated > as > > -250 kJ/mol. > > > > I have triple check my molecules connectivity and the charges and the > > force field. Everything seems to be reasonable. Henceforth, what can > caused > > the extremely high binding energy? > > > > > > Thanks , > > > > > > Ben > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at http://www.gromacs.org/ > Gromacs - Gromacs<http://www.gromacs.org/> > www.gromacs.org > The development of Gromacs would not have been possible without generous > funding support from the European Research Council, the Swedish Research > Council, the Swedish ... > > > > > Support/Mailing_Lists/GMX-Users_List before posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > -- > Billy Noonan* | *PhD Student *|* Bsci ( *Adv* ), IA Hon > > *LinkedIn Profile > <http://www.linkedin.com/profile/preview?locale=en_US& > trk=prof-0-sb-preview-primary-button> > **|* +61420 382 557 > > Monash Institute for Pharmaceutical Sciences ( *MIPS* ) > Royal Parade, Parkville, 3052 > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Billy Noonan* | *PhD Student *|* Bsci ( *Adv* ), IA Hon *LinkedIn Profile <http://www.linkedin.com/profile/preview?locale=en_US&trk=prof-0-sb-preview-primary-button> **|* +61420 382 557 Monash Institute for Pharmaceutical Sciences ( *MIPS* ) Royal Parade, Parkville, 3052 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.