On 10/30/12 3:28 AM, Bharath K. Srikanth wrote:
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?
Do not manually resize the box. Use editconf -box and -center as appropriate to
place all your components within the unit cell. While it may appear from
visualization that your molecules are where you want them to be, they are not.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
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
