2015-10-28 21:53 GMT-06:00 Pallavi Banerjee <[email protected]>: > Thanks a lot! > > Also, I see in all the tutorials that there's no Temperature coupling while > the iterations happen. I don't really understand the rationale behind this. > Aren't the iterations supposed to be done on an NVT ensemble? All tutorials have integrator = sd which means simulation are done with stochastic dynamics and hence in NVT ensemble.
Christoph > > -Pallavi Banerjee > > > On Wednesday, October 28, 2015 at 12:25:34 AM UTC+5:30, Pallavi Banerjee > wrote: >> >> Hello users, >> >> I intend to do IBI for both bonded and non-bonded interactions. Mine is a >> two-component system, hence I have two mapping files, one for the polymer >> and the other for water. In the hexane ibi-bonded tutorial, only one mapping >> file has been provided in the settings.xml since the system is just hexane. >> >> Below is a segment of the settings.xml. How do I include the two mapping >> files in the '<map>hexane_cg.xml</map> , section? >> >> <equi_time>10</equi_time> >> <!-- grid for table*.xvg !--> >> <table_bins>0.002</table_bins> >> <!-- cut the potential at this value (gromacs bug) --> >> <pot_max>1000000</pot_max> >> <!-- extend the tables to this value --> >> <table_end>2.5</table_end> >> </gromacs> >> <map>hexane_cg.xml</map> >> <!-- these files are copied for each new run --> >> <filelist>grompp.mdp topol.top table.xvg index.ndx</filelist> >> <!-- do so many iterations --> >> <iterations_max>500</iterations_max> >> >> Many Thanks. >> >> -Pallavi Banerjee > > -- > 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 post to this group, send email to [email protected]. > Visit this group at http://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- 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 post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
