On 1/24/20 3:20 PM, Li, Shi wrote:
Dear GMX users, I am new to polymer simulation and want to build a polymer system for Gromacs. I have followed Justin's instruction to make polyethylene by editing the rtp and hdb file. But I have a couple of questions regarding a larger polymer configuration: 1. The example system (polyethylene) only has one repeat unit, is there a way to define the number of repeat unit and then generate the PDB file? I
GROMACS has no ability to build molecules.
am also wondering if there is a way to make the configuration with random torsion? I currently use Gaussview to copy and paste, and the initial PDB is just a linear chain. Like this...^^O^^O^^O^^
Make the linear chain and run a Langevin simulation in the gas phase.
2. Since the PDB file is straightly from Gaussview, the atom names in the file are all in basic form (C, H, O...), in order for the pdb2gmx to work, I have to manually match and replace them according to the .rtp file. For larger repeat unit, is there a better way to do this?
Unfortunately, no. Software that outputs repetitive atom names makes your life a nightmare when actually trying to do a simulation.
-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.