[gmx-users] Applying a Lennard-Jones Gauss potential function for TIP5P water

Greetings, I am simulating a box of TIP5P waters and I would like to know if it is possible to change the standard LJ potential function to a more complex one (LJ-Gauss), while keeping the coulombic interaction standard. The custom potential will act between the oxygen atoms only and has the f

[gmx-users] Re: Applying a Lennard-Jones Gauss potential function for TIP5P water

Thanks Justin, I had a look at the manual regarding tabulated potentials... for clarity, The table values must contain: x, f(x), −f(x), g(x), −g(x), h(x), −h(x). For my function then would f(x) = 1/r g(x) = eps*[(sig/r)^12 - 2*(sig/r)^6] and h(x) = -epsG*[exp-(((r-rG)^2) / (2*sigG^2))] ? A

[gmx-users] Re: Different energy using the identical tpr file

Have you tried the -reprod option? Andrish Fahimeh Baftizadeh wrote > Hello, > > I have a 2 tpr files which are identical. Then I am doing a single step MD > (I put n_step=0) simulation just to compute the total energy of a certain > configuration. > > These tpr files give me different energy

[gmx-users] C6 & C12 parameters for non-bonded interactions using tables

Greetings, I am trying to use tabulated potentials for the VdW interactions between TIP5P water molecules. I have tested my topology file to make sure that it gives reasonable results with the standard table6-12.xvg in the /top folder and C6=4*eps*sig^6 , C12=4*eps*sig^12. I am able to match the

[gmx-users] Re: error in running g_dist

Arunima Shilpi-2 wrote > Respected sir > > I want to calculate the distance between protein and ligand after I have > run the production step. I used the following command.. > > g_dist -s md_0_1.tpr -f md_0_1.xtc -o dist.xvg -n index.ndx > > Groups I selected was > Group 1 (protein) > Group 13

Re: Aw: [gmx-users] C6 & C12 parameters for non-bonded interactions using tables

lloyd riggs wrote >   > > Dear Andrish Reddy, > >   > > Dont know if it works but I have for small molecules just put all the > parmeters within the .top file right below the defaults, instead of user > defined tables, and removed the "forcefieldX/SPC.it

[gmx-users] Re: Tabulated Potentials

O'Neill, David wrote > Hello Users, > > Recently I have been trying to implement the use of tabulated potentials > in GROMACS to an system of argon atoms. > > I run a NVE simulation of 1000 argon atoms and then plot the potential > energy from the output. > > ar.itp : > > [ defaults ] > ; nbfun

[gmx-users] Re: fftw

atila petrosian wrote > Dear gromacs users > > > Why should I install fftw before gromacs installation? > > I want to know exact role of fftw in gromacs calculations. > > Please guide me about that. > > Best wishes > -- > gmx-users mailing list > gmx-users@ > http://lists.gromacs.org/ma