I used g_dipoles to calculate dielectric constant.
g_dipoles -f water.trr -s water.tpr -eps Group 0 ( System) has 768 elements Group 1 ( Protein) has 768 elements Group 2 ( Protein-H) has 256 elements Group 3 ( C-alpha) has 0 elements Group 4 ( Backbone) has 0 elements Group 5 ( MainChain) has 0 elements Group 6 (MainChain+Cb) has 0 elements Group 7 ( MainChain+H) has 0 elements Group 8 ( SideChain) has 768 elements Group 9 ( SideChain-H) has 256 elements Select a group: 0 I selected 0. Nilesh On Mon, May 9, 2011 8:28 am, Justin A. Lemkul wrote: > > > Nilesh Dhumal wrote: > >> 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. > > I also asked how you calculated the dielectric constant. > > > When trying to replicate others' work, it is often most beneficial and > less time-consuming to simply contact the corresponding author of the > paper. They can talk with you directly about methodological details. > > -Justin > > >> 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 >>> >>> >>> >>> >> >> >> > > -- > ======================================== > > > 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
