[gmx-users] Fatal error: Shake block crossing node boundaries

Hello, I got an error message while using 8 processors becuase of Shake block crossing node boundaries. Everything was fine when I used a single processor. Any idea how to ease this problem? Thanks! JW The error message: splitting topology... Walking down the molecule graph to make s

[gmx-users] position and velocity in traj file & Verlet algorithm in GROMACS 3.3

Two questions: (1) What are the positions and velocities stored in trajectory files by gmx3.3? I know the positions must be at current time (at time t), but how about velocities? are they at t-0.5*dt, t+0.5*dt or estimated at time t? If gmx3.3 uses leap-frog form of verlet, velocites at time t ar

[gmx-users] Verlet algorithm in GROMACS

Hi, Seems GROMACS implements leap-frog version. What are the stored quantities, are they the current positions and velocities in the trajectory file? How do I restart a simulation at the exact point (position and velocity) of a previous simulaton. Does GROMACSD have velocity Verlet for an alterna

[gmx-users] How to turn off charge groups

we use PME and our results (energy terms) seem depend on the charge group assignment. Based on the manual, the results should not have anything to do with charge groups. How can we turn off the charge groups. Jianwei ___ gmx-users mailing listgmx-u

[gmx-users] How to turn 1-3 interactions on?

Hello, This has something to do with exclusion list. I have a special need and have to turn 1-3 interactions on, that is, I need nobonded interactions (vwd and electrostatic) included in energy calculations for atoms more than one bond away. I have tried the following, seems gmx still exclude