[gmx-users] Dielectric constant for alkanes based on shell polarizable model

Dear Gromacs users, I really hope someone could give me some advise on my following problem.  I am simulating liquid bulk hexane using a shell (or Drude oscillator) model that incorporates the electronic polarization in GROMACS 4.5.3.  To do this, I use the force field parameters from the CHARMM d

[gmx-users] Positive potential energy in simulation using polarizable model

Dear all, This may sound obvious and normally I would know how to address the following question. However, I would like to ask for your opinion. If we are simulating bulk liquid of hydrocarbon using the shell polarizable model, is it possible to have a positive value for the potential energy? In

Re: [gmx-users] Positive potential energy in simulation using polarizable model

simulation? On Sun, Feb 27, 2011 at 11:34 PM, David van der Spoel wrote: > On 2011-02-27 21.20, aldi asmadi wrote: >> >> Dear all, >> >> This may sound obvious and normally I would know how to address the >> following question.  However, I would like to ask for your

Re: [gmx-users] Polarizable halide (Iodide)

Hi David, On Wed, Mar 2, 2011 at 12:12 AM, David van der Spoel wrote: > On 2011-03-01 22.06, Abhijeet Joshi wrote: >> >> Hi all, >> >>            I am trying implement polarizable model for halides >> suggested by Roux group. >> I am not able to equilibrate such system. > "> In present gromacs v

Re: [gmx-users] Surface tension readings in NVT vs NPT simulations

David, I have a question that is still related to your reply. If the bulk liquid NPT and the interfacial liquid-vapor NVT simulations are performed using dispersion corrections to the pressure and energy, while the intefacial liquid-liquid NPAT simulation don't use any correction, can we say that

Re: [gmx-users] Shift functions

Hi Elisabeth, You could check the following paper: D. van der Spoel and P. J. van Maaren. The origin of layer structure artifacts in simulations of liquid water. J. Chem. Theory Comput., 2:1, 2006. Aldi On Fri, Feb 10, 2012 at 4:58 PM, Mark Abraham wrote: > On 11/02/2012 12:52 AM, Elisabeth wro

[gmx-users] PME parameter in GROMACS

Dear all, I would like to know if there is a way in GROMACS to find or specify the value of kappa (or Ewald coupling/splitting parameter) for the PME technique that we use in our simulation. In my case, I would like to perform simulations with a specified kappa value and a grid size of A x A x A f