[gmx-users] calculating lennard-jones interaction

hi dear users  wanna know if the distance between two species is more than the cut off radius of vdw interaction (in a SMD simulation), can we trust the simulation results? I mean what is the difference between this case and the situation that the cut off radius is lower than the distance

[gmx-users] maxwell-boltzmann distribution

Hi dear GROMACS experts I wanna know if GROMACS uses only Maxwell-Boltzmann distribution in statistical mechanics, or it also uses Fermi-Dirac and Bose-Einstein statistics.If it only uses Maxwell-Boltzmann distribution, are the results reliable and correct? I mean can we use this law, which is

[gmx-users] dodecahedron box

hi dear all users I'm simulating 2 proteins in a dodecahedron unit cell,and I want to put these 2 proteins in an exact distance from each other, and also from the boundaries, and I have some questions for doing this. 1) How can I implement this exact distance from the other protein and also the

[gmx-users] positive potential energy

Hi dear all I'm simulating a system containing CNT, when I put CNT in a unit cell and want to run energy minimization in a vacuum, I encounter with such an error: The optimal PME mesh load for parallel simulations is below 0.5   and for highly parallel simulations between 0.25 and 0.33,   for

[gmx-users] Re: positive potential energy

Sorry ...I forget to announce that my potential energy is positive, is it logical? From: Zahra M s_zahra_mous...@yahoo.com To: gmx-users@gromacs.org gmx-users@gromacs.org Sent: Thursday, December 29, 2011 12:52 PM Subject: positive potential energy Hi dear

[gmx-users] Re: gmx-users Digest, Vol 92, Issue 138

, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics:   1. Re: -pbc nojump (mohammad agha)   2. positive potential energy (Zahra M)   3. Re: positive potential energy (Zahra M)   4. Re: Re: positive potential energy (Mark Abraham