On 8/20/19 5:21 AM, Jorden Cabal wrote:
Hi Justin, Thank you for your response. In my case the cost of increasing simulation box is very large. I have already tried it by keeping distance between the periodic images of the macromolecule up to 50 Angstrom. Could you suggest me any other option to do this. In Gromacs, rotation around pivot can be enforced, is it possible to use this method somehow to counter the rotation? Even if its possible, how and to which extent do you think it will add biasness to the independent behavior of the macromolecule. Any suggestions, comments in this regard will help me.
You can apply biasing potentials to avoid rotation, but then you're seriously perturbing the dynamics in a way that might completely bias your results (I don't have nearly enough context to say for sure, so I'll be a bit circumspect). If you have a large molecule that rotates, you need a large box that reflects that intrinsic symmetry. It's the same reason you can't build a long, rectangular box around a DNA duplex. If it rotations orthogonal to the longest axis, it sees it's image and the forces are invalid.
There are no real "tricks" here. If you have a big molecule, you need a suitably large box.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 [email protected] | (540) 231-3129 http://www.thelemkullab.com ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
