---------- Forwarded message ---------- From: Amir Marcovitz <[email protected]> Date: Mon, Jan 4, 2010 at 6:18 PM Subject: mdrun error To: [email protected]
Hi, my system is composed of 2 molecules that are arranged in a lattice: i.e., each molecule is represented by 4 atoms (which are charged) and organized in a square lattice. bonds, angles and dihedrals connect the 4 atoms on each lattice. i want to simulate the 2 'plates' such that they are parallel so i added 90 degrees, inter-lattice angles between selected atoms in the system to the [angles] section in the *.top file the processing with grompp worked fine but the mdrun aborted with the following error: *------------------------------------------------------- Program mdrun, VERSION 4.0.5 Source code file: nsgrid.c, line: 348* *Fatal error: Number of grid cells is zero. Probably the system and box collapsed.* *------------------------------------------------------- * beforehand the following massages poped-up: * t = 2.954 ps: Water molecule starting at atom 9891 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates* ** and* * ** *Step 1478 Warning: pressure scaling more than 1%, mu: 1.95218 1.95218 1.95218* ** does anyone has a clue of what is wrong? Thanks, Amir
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