[gmx-users] VdW and Coulomb SR contribution to dVdl in thermodynamic integration
Oh dear, yes I do use a soft core potential and I overlooked that I set sc-power to 1. So even at lamda=0 there should be a soft core contribution to dV/dl! Thanks Berk. >I guess you are using soft-core interactions. >In that case there are more terms in dV/dl, see eq. 4.120 in the manual. Berk. >> Date: Mon, 14 Apr 2008 18:13:32 +0200 >> From: reich at mpikg.mpg.de >> To: gmx-users at gromacs.org >> Subject: [gmx-users] VdW and Coulomb SR contribution to dVdl in thermodynamic integration >> >> Dear Gromacs-users, >> >> I have been doing a test thermodynamic integration for the conversion of >> methanol into a dummy molecule in water. I have been interested in the contribution of the VdW and Coulomb short range interaction to dVdl. According to equations 4.108 and 4.104, at lambda=0 (the methanol-state) >> the contributions should be the negative Lennard-Jones and Coulomb short >> range interaction energies between methanol and the surrounding water. I >> have been calculating the interaction energies with g_energy (choosing LJ-SR:methanol-rest and Coul-SR:methanol-rest as options). For example for >> a particular step in my trajectory I get >> >> -7.954321 kJ/mol for the Lennard-Jones interaction >> >> and -56.966656 kJ/mol for the Coulomb intercation between methanol and water. >> >> So the contribution of the combined interactions to dVdl should be >> >> 64.921 kJ/mol >> >> >> I have, however, also used the option sepdvdl with mdrun to get some detailed information on dVdl during the simulation. >> The line from the log-file giving me the contribution of Lennard-Jones and >> Coulomb short range interactions for the simulation step in question is: >> >> VdW and Coulomb SR particle-p. V -1.49467e+04 dVdl 1.01145e+03 >> >> So the simulation output gives me a result that is two magnitudes greater >> than what I calculated! Is there anything wrong with my reasoning or do you have any other clue why I end up with two different results? >> >> >> Thanks >> >> Luther ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] VdW and Coulomb SR contribution to dVdl in thermodynamic integration
I guess you are using soft-core interactions. In that case there are more terms in dV/dl, see eq. 4.120 in the manual. Berk. > Date: Mon, 14 Apr 2008 18:13:32 +0200 > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Subject: [gmx-users] VdW and Coulomb SR contribution to dVdl in thermodynamic > integration > > Dear Gromacs-users, > > I have been doing a test thermodynamic integration for the conversion of > methanol into a dummy molecule in water. I have been interested in the > contribution of the VdW and Coulomb short range interaction to dVdl. > According to equations 4.108 and 4.104, at lambda=0 (the methanol-state) > the contributions should be the negative Lennard-Jones and Coulomb short > range interaction energies between methanol and the surrounding water. I > have been calculating the interaction energies with g_energy (choosing > LJ-SR:methanol-rest and Coul-SR:methanol-rest as options). For example for > a particular step in my trajectory I get > > -7.954321 kJ/mol for the Lennard-Jones interaction > > and -56.966656 kJ/mol for the Coulomb intercation between methanol and water. > > So the contribution of the combined interactions to dVdl should be > > 64.921 kJ/mol > > > I have, however, also used the option sepdvdl with mdrun to get some > detailed information on dVdl during the simulation. > The line from the log-file giving me the contribution of Lennard-Jones and > Coulomb short range interactions for the simulation step in question is: > > VdW and Coulomb SR particle-p. V -1.49467e+04 dVdl 1.01145e+03 > > So the simulation output gives me a result that is two magnitudes greater > than what I calculated! Is there anything wrong with my reasoning or do > you have any other clue why I end up with two different results? > > > Thanks > > Luther > > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] VdW and Coulomb SR contribution to dVdl in thermodynamic integration
Dear Gromacs-users, I have been doing a test thermodynamic integration for the conversion of methanol into a dummy molecule in water. I have been interested in the contribution of the VdW and Coulomb short range interaction to dVdl. According to equations 4.108 and 4.104, at lambda=0 (the methanol-state) the contributions should be the negative Lennard-Jones and Coulomb short range interaction energies between methanol and the surrounding water. I have been calculating the interaction energies with g_energy (choosing LJ-SR:methanol-rest and Coul-SR:methanol-rest as options). For example for a particular step in my trajectory I get -7.954321 kJ/mol for the Lennard-Jones interaction and -56.966656 kJ/mol for the Coulomb intercation between methanol and water. So the contribution of the combined interactions to dVdl should be 64.921 kJ/mol I have, however, also used the option sepdvdl with mdrun to get some detailed information on dVdl during the simulation. The line from the log-file giving me the contribution of Lennard-Jones and Coulomb short range interactions for the simulation step in question is: VdW and Coulomb SR particle-p. V -1.49467e+04 dVdl 1.01145e+03 So the simulation output gives me a result that is two magnitudes greater than what I calculated! Is there anything wrong with my reasoning or do you have any other clue why I end up with two different results? Thanks Luther ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
