This is continuation to my previous mail. I am trying to simulate a molecule using mdrun but i am getting errors.After 2 steps i got " Warning: 1-4 interaction between 245 and 251 at distance 1.922 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation. This usually means your system is exploding, if not, you should increase table-extension in your mdp file. " and then finally the program is quitting giving the message. "Number of grid cells is zero. Probably the system and box collapsed" i am unable to sort out the real problem of this.I have tried increasing the grid size and also table-extension,but still i am getting the same message. Can someone suggest me where i am going wrong and what is to be done???Is this problem because of the compiler???
Hi Ramya, I have observed similar problem with another protein. It seems not an issue with the program, but with the protein. U can try running again after a short geometry optimization of the protein (eg: minimization with Argus lab tool). This usually happens for proteins with bad Ramachandran plots. See that also. Good luck. -- M.N. MANOJ PROJECT LEADER - BIOINFORMATICS VITTAL MALLYA SCIENTIFIC RESEARCH FOUNDATION BANGALORE INDIA
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