Hi guys, 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.
Converged to machine precision, but not to the requested precision Fmax < 100 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Back Off! I just backed up sys_EM_ready.gro to ./#sys_EM_ready.gro.2# Steepest Descents converged to machine precision in 499 steps, but did not reach the requested Fmax < 100. Potential Energy = -1.2830664e+06 Maximum force = 3.4162991e+03 on atom 2 Norm of force = 3.2566280e+01 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. My questions: -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? -How I can improve on EM, what kinda setting in mdp file can I use to that system converges even after 10,000 steps? -How to prevent clashes, maybe there are some settings to try with genbox -cp -cs command? Thanks
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