On Thu, May 25, 2023 at 7:23 AM Kankana Bhattacharjee <[email protected]> wrote: > > Dear Sir, > > I am learning votca. Now, I have done spce water model atomistic md run. In > the spce/atomistic foolder, grompp.mdp contains integrator as "sd" . And, I > used this settings for short MD run. Then, used csg_tool to compute rdf of > CG-CG beads and compared with CG-CG with ibi. Then, I dint understand the > "Running ibi" part of the spce model. It has been asked to reduce the number > of MD steps in grompp.mdp and adjust the equilibration time in the > settings.xml file. Exactly how to adjust this and why ? I have skipped the > "Running ibi" option.
Well, the number of MD steps is in grompp.mdp, while the equilibration time is in settings.xml. Longer run will give you smoother RDFs, and the system usually needs some time to equilibrate from the initial condition, so you don't want to pick that too short. In the tutorial we ask folks to explore these options to get some feel for statistics. > > Second;y, I did force matching part exactly. But, dint understand exactly > what is happening. Like, If I want to generate gromacs compatible > forcefield.itp for a coarse grained model and perform MD simulation using > gromacs. THen, how can I generate ttp file for a molecule. Force matching return a tabulated force that can then be used to run the coarse-grained simulation. Have a look at the topol.top of the spce/ibi example. Christoph > > Thanks & Regards > Kankana Bhattacharjee > > -- > Join us on Slack: https://join.slack.com/t/votca/signup > --- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To view this discussion on the web visit > https://groups.google.com/d/msgid/votca/c6eaf8c8-1963-4772-9800-dc9d839dd0bbn%40googlegroups.com. -- Christoph Junghans Web: http://www.compphys.de -- Join us on Slack: https://join.slack.com/t/votca/signup --- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/votca/CAHG27e73xWx4bDHzx2AAxA%2B8OaQC%2B_6ru%2B7iACRsRWZrDJOoqQ%40mail.gmail.com.
