Hi guys,<br><br>I am trying to start simulation on lipid - peptide system, but receive LINCS warnings of angles rotating more than 30 deg which means that my system is unstable. I have tried to do mdrun on the DMPC box itself and had no problems. Once I insert my peptide, the problems starts. I have run Energy MInimization with LIncs order or 4 and Lincs iterations 8, but still could not bring system to 200 kJ/mol Fmax. Received the following message.<br>
<br>Converged to machine precision,<br>but not to the requested precision Fmax < 100<br><br>Double precision normally gives you higher accuracy.<br>You might need to increase your constraint accuracy, or turn<br>off constraints alltogether (set constraints = none in mdp file)<br>
<br>writing lowest energy coordinates.<br><br>Back Off! I just backed up sys_EM_ready.gro to ./#sys_EM_ready.gro.2#<br><br>Steepest Descents converged to machine precision in 499 steps,<br>but did not reach the requested Fmax < 100.<br>
Potential Energy = -1.2830664e+06<br>Maximum force = 3.4162991e+03 on atom 2<br>Norm of force = 3.2566280e+01<br><br>Now I am trying to just to do EM (energ. minim) on my 14 aa peptide, in water box just to see if it will work.<br>
<br>My questions:<br>-How to position peptide into existing lipid box (apart form using editconf -rotate parameter). I have tried VMD and did it visually, but new coordingates were not saved?<br>-How I can improve on EM, what kinda setting in mdp file can I use to that system converges even after 10,000 steps?<br>
-How to prevent clashes, maybe there are some settings to try with genbox -cp -cs command?<br><br>Thanks<br>