HI Chandan, 2012/11/14 Chandan Choudhury <[email protected]>: > > Dear votca users, > > I have just started using votca with Gromacs 4.5.5 and was trying out the > examples in the src directory. Welcome the the mailing lists. > > In the hexane tutorial, I have understood and executed the run.sh script. > When I browse the ibi and ibi_nonbonded directories, I find the table and > potential (bond and angle) files. > > How can these files be generated? This will help me to understand the flow > of votca. For the general workflow, please have a look at our manual.
But in short it breaks down to: 1.) Run the atomistic simulation (mdrun call in atomistic/run.sh) 2.) Calculate distributions from the atomistic simulation (csg_stat call in atomistic/run.sh) 2a.) For IBI of non-bonded interaction the rdf (see ibi/*.dist.tgt) is already the input. 2b.) For bonded IBI you will have to invert the distributions to obtain an initial guess (see ibi_bonded/*.pot.in). (There is a whole manual section and an extensive thread on this mailing list on how to do that with csg_call or csg_boltzmann.) 3.) Run IBI simulations Christoph > > > Chandan > -- > Chandan kumar Choudhury > National Chemical Laboratory, Pune > INDIA > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]. > For more options, visit this group at > http://groups.google.com/group/votca?hl=en. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/votca?hl=en.
