in 5 ns final mdrun in MD simulation after 1.9 ns system exits & error coming like bond length not finite. I have reduced the dt from 2 fs to 1 fs in md.mdp file and 500 ps of NVT NPT equillibriation was done once again but still that error is coming.how to solve it?
Please paste the complete message and the protocol you followed until the production run. Any errors during npt equilibration?
I have used position restraints throughout the simulation for my probe molecule after energy minimization. I have worked with some non standered residue and run 100 ps position restraint mdp file,then equllibriate in NVT ensemble for 500 ps at 300 K,then NPT for 500 ps at 1 bar, at last using the gro file after NPT as input file for final mdrun I have tried to run it for 5 ns but after 1.9 ns it exits giving that error.There was no error in the NVT NPT step.
I would suggest to monitor the energy of non-standard residue. Try to check the structure (specifically non-standard residue) before crash. It might be possible that something is wrong with force-field parameters of non-standard residue.
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