Hi There, I was trying to run a equilibrium run (npt) for system of "Methane in 1-octanol" (1 methane molecule with 200 1-octanol molecules with OPLS FF parameters). Following is the series of steps I followed: 1. Energy minimization with steep integrator for 5000 steps 2. Energy minimization with l-bfgs integrator for 5000 steps 3. NVT run for 100 ps with sd integrator 4. NPT run for 100 ps with sd integrator (with Pcoupl = Parrinello-Rahman, tau_p = 0.5, compressibility = 4.5e-05, ref_p = 1.0)
During the NPT run I am ending up with following error (too many LINCS warning): --------------------------------------------- Step 25406, time 50.812 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 11.778495, max 363.475445 (between atoms 2158 and 2157) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2152 2150 90.0 0.1090 1.3690 0.1090 2152 2151 90.0 0.1090 36.5266 0.1090 2158 2156 90.0 0.1091 0.5637 0.1090 2158 2157 90.0 0.2349 39.7278 0.1090 Back Off! I just backed up step25406b_n0.pdb to ./#step25406b_n0.pdb.1# Back Off! I just backed up step25406c_n0.pdb to ./#step25406c_n0.pdb.1# Wrote pdb files with previous and current coordinates Segmentation fault ------------------------------------------------------------ *.mdp files for above simulation are adapted from tutorial on free energy calculation by Justin. Please suggest me what could be wrong with above simulation. Regards, Vivek Sharma
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