Hi There,<br> 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:<br>
1. Energy minimization with steep integrator for 5000 steps <br>2. Energy minimization with l-bfgs integrator for 5000 steps<br>3. NVT run for 100 ps with sd integrator <br>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)<br>
<br>During the NPT run I am ending up with following error (too many LINCS warning):<br>---------------------------------------------<br>Step 25406, time 50.812 (ps) LINCS WARNING<br>relative constraint deviation after LINCS:<br>
rms 11.778495, max 363.475445 (between atoms 2158 and 2157)<br>bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br> 2152 2150 90.0 0.1090 1.3690 0.1090<br>
2152 2151 90.0 0.1090 36.5266 0.1090<br> 2158 2156 90.0 0.1091 0.5637 0.1090<br> 2158 2157 90.0 0.2349 39.7278 0.1090<br><br>Back Off! I just backed up step25406b_n0.pdb to ./#step25406b_n0.pdb.1#<br>
<br>Back Off! I just backed up step25406c_n0.pdb to ./#step25406c_n0.pdb.1#<br>Wrote pdb files with previous and current coordinates<br>Segmentation fault<br>------------------------------------------------------------<br>
<br>*.mdp files for above simulation are adapted from tutorial on free energy calculation by Justin.<br><br>Please suggest me what could be wrong with above simulation.<br><br>Regards,<br>Vivek Sharma<br><br><br>