>>> Dear Gmx-users, >>> I am simulating a carbon nanotube in vaccum (NVE ensemble). I have taken >>> parameters of carbon nanotube from "Strong correlations and Fickian >>> water water >>> diffusion in narrow carbon nanotube, Biswaroop Mukherjee, Prabal K. >>> Maiti Chandan >>> Dasgupta and A. K. Sood, JCP, 126 124704 (2007)". >>> During the run my carbon nanotube does not remain cylindrical, it >>> bends inwards and forms >>> a dumbell shaped structure, also it rotates in space and does not >>> remain fixed. >>> My questions are >>> 1) are my itp and mdp parameters correct >> >> Formally correct. >> > > Flexible water should not be used for MD.
what do you mean? >All the water models in Gromacs > should be rigid. As such, "define = -DFLEXIBLE" is incorrect. where did water come from? he said "I am simulating a carbon nanotube in vaccum (NVE ensemble)" >>> 2) how do i determine if system is really in ground state or stable >> >> You CNT should not migrate within a box, for sure. I believe it is >> principally impossible in spite of the force field parameters that can >> be used. You may want to upload the video with the system dynamics on >> the YOUTUBE for us to look at. >> >> >>> 3) temprature keeps on rising as the simulation proceeds is this all >>> right? >> >> No. For how much does it increase? >> > > Using a plain cutoff for the electrostatics could be causing this. > > -Justin > >> >> -- >> Dr. Vitaly Chaban > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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 [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
