Dear All, I'm simulating a empty membrane (128POPC + 2460 water) , the structure obtained from Tielemen's website. Thanks for the help from Justin and Mark, the structure had minimized and stop at 217steps
Energies (kJ/mol) Bond Angle Proper Dih. Ryckaert-Bell. Improper Dih. 5.20262e+03 1.01146e+04 4.17230e+03 3.36598e+03 7.50236e+02 LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. 4.01104e+03 8.22333e+03 -1.49543e+04 -1.31978e+05 -1.41296e+05 Potential Kinetic En. Total Energy Temperature Pressure (bar) -2.52387e+05 0.00000e+00 -2.52387e+05 0.00000e+00 0.00000e+00 Steepest Descents converged to Fmax < 1000 in 217 steps Potential Energy = -2.52387473541938e+05 Maximum force = 9.30404466610315e+02 on atom 5631 Norm of force = 5.34591310731597e+03 The trajectory and energy seems ok. 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. Subsequently, i moved on with NPT and it stopped due to LINCS warning as below:- Step 269, time 0.538 (ps) LINCS WARNING relative constraint deviation after LINCS: max inf (between atoms 1980 and 1981) rms inf bonds that rotated more than 30 degrees: 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, the structure is well equilibrated. What is the reason for this? Is it something which i missed out during NVT or NPT? Please advice. Regards, Bing
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