Hi, my name is Lazaro. I have done calculations using QM methods. But I am starting now to learn MD and I am using Gromacs 2020.1. I want to run simulations in vacuum for small deoxynucleosides and ribonucleosides (around 32 atoms) with the finality to initially optimize these molecules relaxing all position (find the most stable structure) to use this structure as input for DFT calculations in the future.
I have study from the manual and the gromacs.org_gmx-users@maillist.sys.kth.se tutorials and have successfully run a couple of simulations of the adenosine in water environment. But when I try to run the simulation in vacuum I have some problems. If I create a box, but from there instead of fill it with water I go directly and try to do an energy minimization, when I visualize the potential it decrease but the curve does not look like the examples or like when I do the simulation in vacuum. Do you think this is correct? or is correct how I am proceeding? Should I modified the .mdp? Appreciating any help in advance kindly, Lazaro -- 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.
