Dear All,<br>I'm simulating a empty membrane (128POPC + 2460 water) , the structure obtained from Tielemen's website. <br>Thanks for the help from Justin and Mark, the structure had minimized and stop at 217steps<br>
<br>Energies (kJ/mol)<br> Bond Angle Proper Dih. Ryckaert-Bell. Improper Dih.<br> 5.20262e+03 1.01146e+04 4.17230e+03 3.36598e+03 7.50236e+02<br> LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip.<br>
4.01104e+03 8.22333e+03 -1.49543e+04 -1.31978e+05 -1.41296e+05<br> Potential Kinetic En. Total Energy Temperature Pressure (bar)<br> -2.52387e+05 0.00000e+00 -2.52387e+05 0.00000e+00 0.00000e+00<br>
<br><br>Steepest Descents converged to Fmax < 1000 in 217 steps<br>Potential Energy = -2.52387473541938e+05<br>Maximum force = 9.30404466610315e+02 on atom 5631<br>Norm of force = 5.34591310731597e+03<br><br>
The trajectory and energy seems ok.<br><br>With this, i proceed with NVT, although by looking at the energy and temperature (300K) graph after NVT both looks fine. But when i tried to look at the trajectory, i noticed that the upper layer lipid and lower layer lapid actually moved further away from each other as compared to the starting structure. And i don't know what cause this to happen. Please advice.<br>
Subsequently, i moved on with NPT and it stopped due to LINCS warning as below:-<br><br>Step 269, time 0.538 (ps) LINCS WARNING<br>relative constraint deviation after LINCS:<br>max inf (between atoms 1980 and 1981) rms inf<br>
bonds that rotated more than 30 degrees:<br><br>This mean that some of the atoms in the structure is moving and it is out of the cutt-off which being defined, it also said that it might due to the reason that the starting structure is not equilibrated or many overlaps. But as what i know,<br>
the structure is well equilibrated. What is the reason for this? Is it something which i missed out during NVT or NPT? Please advice.<br><br><br>Regards,<br>Bing <br><br><br><br>