Hi Chris My EM works just fine if I use a cubical box of water, so I'm baffled as to what's going wrong in this case.
I tried the entire process again, this time removing position restraints. Let me describe my entire procedure on this occasion, once again: 1) I first assembled a bilayer of 128 DOPC lipids, in a box of dimension 7.5 x 7.5 x 7.5 nm3. 2) I then removed the water molecules, resized the box length by changing the bottom line of the coordinate file, and inserted a CNP to an appropriate location, about 7 nm above the bilayer. 3) Then, I performed an energy minimization, and the CNP did not move about. So far, so good. 4) I solvated the box with water using genbox, and then attempted an energy minimization (using steepest descents). This is where the problem arises. These are the coordinates from the input coordinate file, before the energy minimization: 129F16 C01 1793 10.600 3.474 3.330 129F16 C02 1794 10.438 3.758 3.294 129F16 C03 1795 10.381 3.588 3.947 129F16 C04 1796 10.795 3.703 3.387 129F16 C05 1797 10.564 3.308 3.584 129F16 C06 1798 10.289 3.506 3.415 129F16 C07 1799 10.322 3.939 3.528 129F16 C08 1800 10.655 3.430 3.872 129F16 C09 1801 10.840 3.479 3.620 129F16 C10 1802 10.641 3.958 3.453 129F16 C11 1803 10.342 3.876 3.850 129F16 C12 1804 10.610 3.991 3.756 129F16 C13 1805 10.675 3.736 3.950 129F16 C14 1806 10.307 3.397 3.721 129F16 C15 1807 10.862 3.787 3.699 129F16 C16 1808 10.172 3.686 3.649 And these are the coordinates from the output coordinate file, within just TEN steps of energy minimization: 4849F16 C01 6513 1.015 0.049 5.350 4849F16 C02 6514 1.294 -3.135 4.063 4849F16 C03 6515 0.663 -1.872 3.948 4849F16 C04 6516 1.521 -1.365 3.815 4849F16 C05 6517 2.111 -0.464 4.030 4849F16 C06 6518 0.546 -2.205 6.177 4849F16 C07 6519 -0.418 -2.289 6.608 4849F16 C08 6520 -0.301 -1.054 4.991 4849F16 C09 6521 -0.154 -1.757 5.881 4849F16 C10 6522 0.595 -0.223 5.592 4849F16 C11 6523 1.450 -0.980 7.148 4849F16 C12 6524 0.055 -1.027 5.487 4849F16 C13 6525 0.020 -0.473 5.753 4849F16 C14 6526 1.492 -0.255 4.474 4849F16 C15 6527 0.926 -0.762 4.489 4849F16 C16 6528 0.147 -2.022 3.748 I have no idea why this is happening- that the molecule could move so much seems ridiculous. Besides the em.mdp file, is something wrong with, for example, my method of resizing the box? Thanks! Bharath --original message-- Sorry Bharath, I simply can not believe that a macromolecule drifted 3 nm during energy minimization. What happened to the intervening solvent? I think that you have some problem with your technique here. Why did you use 120 constraints? Is this for bonds within the CNP? You need to do 2 things: a) figure out what is going wrong with your EM... what you describe seems impossible to me. b) simplify your system to debug the problem. So you get the same warnings about too many constraints if you omit the position restraints? Chris. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
