On Fri, Nov 16, 2012 at 12:10 AM, Christoph Junghans <[email protected]>wrote:
> 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. > Thanks. > > > > 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 > Thanks Christoph for the lucid explanation. The bonded distributions are inverted and by using series of votca scripts ( https://groups.google.com/d/msg/votca/OSaBKQTR7C0/_dtF93DJZP0J), I could obtain the bond and angle tabulated potentials. I am at present looking at the hexane tutorials. One query regarding this is that how do I understand that the tabulated potentials generated are correct. [As I have simulated (atomistic) for just 6 ns, the potentials (table_a1.xvg and table_b1.xvg) do not match to the ones present in the tutorial.] Chandan > > 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. > > -- Chandan kumar Choudhury NCL, 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.
