[gmx-users] Reaction field zero, ions, twin-range and LIE

Hello users For making a rerun of a MD simulation done with PME, but this time using Reaction field zero, do I eliminate the ions from the system, previously added to neutralize and ran with PME? What do you think about using a twin-range cut off instead of reaction field zero? I need to obtain pre

[gmx-users] reaction field

Hello I would like to perform a molecular simulation with the AMBER99SB FF , tip3p water model and reaction field for long range interactions. Which value of epsilon_rf (The relative dielectric constant of the reaction field) do I have to use? Thanks Williams -- gmx-users mailing listgmx-us

Re: [gmx-users] reaction field kappa and ionic strength

Daniela S. Mueller wrote: dear all, there are errors in the code regarding 1) the equation for kappa, which is used for the reaction field method; and 2) in the calculation of the ionic strength. 1) in rf_util.c kappa is calculated as *kappa = sqrt(2*I/(EPSILON0*eps_rf*BOLTZ*Temp)); but th

[gmx-users] reaction field kappa and ionic strength

dear all, there are errors in the code regarding 1) the equation for kappa, which is used for the reaction field method; and 2) in the calculation of the ionic strength. 1) in rf_util.c kappa is calculated as *kappa = sqrt(2*I/(EPSILON0*eps_rf*BOLTZ*Temp)); but the factor 2 in the square ro

[gmx-users] Reaction field: Berendsen or Nose-Hoover thermostat?

Dear community, I am currently running REMD with reaction field. I started with the berendsen thermostat, and my md average temperatures were 10 to 15K warmer than the ones specified in the input file. I had thermostat time coupling constants of 0.1 for the protein and 0.4 for the solvent