On 9/5/19 3:07 AM, Srijan Chatterjee wrote:
Hi Justin, "The force fields in GROMACS are (by design) biomolecular in nature. None support tungsten." Thanks for clarifying. I happen to just come across a paper with similar forcefield values (https://doi.org/10.1016/j.jct.2019.01.016) Although there is another problem with this molecule because of its octahedral geometry. It contains several 180-degree bonds. So as from my understanding of the CO2 tutorial gromacs has had difficulty in dealing 180-degree bond. So, my question is 1) Do I have to use a virtual site to constrain the molecular geometry? If so, for an octahedral geometry what should I do? 2) Is there any other way of doing it other than virtual site?
Try using the 180-degree angle. I wrote the virtual site tutorial when GROMACS could not handle such a case but I believe the code changed some time ago.
3)If I perform position restraint to each atom of 10000 still I can see some movement of atoms but the molecule is not breaking. Is it bad or reasonable approach to do it during MD?
10000 is a rather strong force constant, but as with any restraint, it will never prevent motion, only disfavor it.
-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 jalem...@vt.edu | (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 gmx-users-requ...@gromacs.org.
