Re: [gmx-users] ambar to opls force field

Nilesh Dhumal wrote: 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 elem

Re: [gmx-users] ambar to opls force field

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 (Bac

Re: [gmx-users] ambar to opls force field

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

Re: [gmx-users] ambar to opls force field

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 ha

Re: [gmx-users] ambar to opls force field

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 past

Re: [gmx-users] ambar to opls force field

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

Re: [gmx-users] ambar to opls force field

Nilesh Dhumal wrote: Thanks Justin. I am using flexibale water model for my system. I am refering a paper J. Chem. Phys. 124, 024503 (2006). Author have used Amber type force field. i.e. 1/2 Kbond (r-req)**2 + 1/2 Kangle(theta-thetaeq)**2. Kbond = 443153.3808 kJ/mol nm**2 Kangle= 317.5656 k

Re: [gmx-users] ambar to opls force field

Thanks Justin. I am using flexibale water model for my system. I am refering a paper J. Chem. Phys. 124, 024503 (2006). Author have used Amber type force field. i.e. 1/2 Kbond (r-req)**2 + 1/2 Kangle(theta-thetaeq)**2. Kbond = 443153.3808 kJ/mol nm**2 Kangle= 317.5656 kJ/mol rad**2. I am using

Re: [gmx-users] ambar to opls force field

On 7/05/2011 8:10 AM, Nilesh Dhumal wrote: Hello, How can I convert ambar force field to opls force field. Should I half the force constant of bond (Ka) and angle (Kb)? Having read the papers describing how their bonded interactions work, shouldn't you know how to convert them? Having a g

Re: [gmx-users] ambar to opls force field

Nilesh Dhumal wrote: Hello, How can I convert ambar force field to opls force field. Should I half the force constant of bond (Ka) and angle (Kb)? Why would you do that? Most of the bonded parameters in OPLS were taken from AMBER directly, IIRC. If you need to parameterize some new bon

[gmx-users] ambar to opls force field

Hello, How can I convert ambar force field to opls force field. Should I half the force constant of bond (Ka) and angle (Kb)? NIlesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/