[gmx-users] LJ fluid

HI gromacs users, in order to simulate Argon fluid i use epsilon=m=sigma=1, so the parameters for the LJ are 4.000 4.000the question is what reduced time step (t*)is appropriate for MD, what coupling methods for temperature and pressure and what the value for nrexcl for the Ar atomsthanks in

Re: [gmx-users] LJ fluid

Argyrios Karatrantos wrote: HI gromacs users, in order to simulate Argon fluid i use epsilon=m=sigma=1, so the parameters for the LJ are 4.000 4.000 the question is what reduced time step (t*) is appropriate for MD, what coupling methods for temperature and pressure and what the value for

[gmx-users] (dH/dl) calculation

Dear experts I am doing FEP (thermodynamic integration method) simulations. I have a questions about dH/dl calculation in GROMACS. Take in mind equation 3.77 from the GROMACS 3.3 manual. There, dA/dl is calculated as dA/dl = SS{ (dH/dl) exp()dp dq } / SS{ exp()dp dq = dA/dlNVT;l } where SS are

[gmx-users] conversion gromos gromacs

Hi, I need to convert GROMOS topology file into GROMACS format, I wonder if someone know of a program in GROMACS or GROMOS packages that does it. Thanks, Itamar -- Prediction is very difficult, especially about the future - Niels Bohr ___ gmx-users

[gmx-users] Simulation single unit of a dimer

Dear gmxions, The protein, which I am going to simulate, is a dimer, but my study through MD is not related of dimer interaction but its catalytic activity. So my question is can I simulate a unit of the dimer? Will that system be physically right to simulate? The individual unit of the dimer is

[gmx-users] no temperature coupling

Dear GROMACS developers,I would like to do a SPC-water simulation without temperature coupling. I set tcouple to 300K and did Berenderson T-coupling first for 400 ps to equilibrate the system. Then I copy confout.gro to conf.gro, set tcoupl to no. However the Temperature of the later similation