On 7/8/19 3:22 AM, afsaneh maleki wrote:
Hi all I have two questions: 1- Is it correct to apply statistical ensemble NVT (N=constant, T=constant) for simulating of carbon nanotube (as drug delivery)? It doesn’t leads to a pressure in the system that is far from normal pressure? Some Author use VNT and the other use NPT. In the other word, when we can use NVT ensemble to simulation CNT (as drug delivery)?
The ensemble should be chosen based on which conditions are relevant to the simulation. Perhaps some people use NVT simply to side-step any possibility of compression along the CNT axis; sometimes models are simplified in this way. Perhaps that's not the most accurate. That's your job to decide what is the best model for the questions you are trying to answer.
2- How to distinguish between infinite CNT and finite CNT with command in .mdp file?
The main difference is in the topology, but in the case of an infinite CNT, you must use "periodic_molecules = yes" in the .mdp file. Proper bonds must be specified in the topology.
-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.
