Hello Justin, In the J. Chem. Phys. paper author have run the simulation 6.5 ns. So
I run the simulation 6.5 ns for collecting data and I have total 256 water molecules. NIlesh On Sun, May 8, 2011 11:58 pm, Justin A. Lemkul wrote: > > > Nilesh Dhumal wrote: > >> Hello Justin, >> >> >> Here I have done some analysis. The original value reported in J.Chem. >> Phys. 124, 024503 2006, paper are >> Kbond = 443153.3808 kJ/mol nm**2 >> Kangle = 317.5656 kJ/mol rad**2. >> >> >> >> Below are the results for the dielectric constant of water.I made the >> .itp >> file pasted below the table. Bond length is nm. >> >> bond length Kbond angle Kangle dielectric constant 0.1012 >> 443153.3808 113.24 317.5656 ~1.9 : orginal value >> >> >> 0.1012 221576.6904 113.24 317.5656 ~80 : 1/2 (Kbond) >> >> >> 0.1012 443153.3808 113.24 158.7828 ~1.58 : 1/2 (kangle) >> >> >> 0.1012 221576.6904 113.24 317.5656 ~1.9 : 1/2 >> (Kbond)&(Kangle) >> >> > > How were these dielectric constants calculated? Did you collect > sufficient data? It seems to me that there is no definitive dependence on > any of these parameters, and you have one outlying point that is > coincidentally close to what you want. A consistently wrong dielectric > would suggest that either you're not calculating it right or you don't > have sufficiently converged data. > > Based on a quick look through the paper, it seems to me that your > original premise of converting between force fields is not related to the > task at hand. Water models are relatively force field-agnostic, especially > when trivial functional forms, such as harmonic potentials, are applied. > There is nothing > fancy here. > > Given the following: > > >> [ bondtypes ] >> ; i j func b0 kb >> OW HW 1 0.1012 443153.3808 ; J. Chem. Phys. >> (2006),124,024503 >> [ angletypes ] >> ; i j k func th0 cth >> HW OW HW 1 113.24 158.7828 ; J. Chem. Phys. >> (2006),124,024503 >> >> > > You are indeed applying simple harmonic potentials (see the manual to > confirm the form), which again indicates to me that you should not be > playing with the force constants in the model described in the paper. Use > Ka and Kb as listed. > Halving these quantities will result in a harmonic potential, e.g. for > bonds of (1/4)Kb(b-b0)^2 rather then the proper coefficient of 1/2. > > > -Justin > > > -- > ======================================== > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read > http://www.gromacs.org/Support/Mailing_Lists > > > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
