2015-10-29 10:58 GMT-06:00 Pallavi Banerjee <pallavis...@students.iiserpune.ac.in>: > Speaking of sd, would the results be affected a lot on using md integrator > with V-rescale as the thermostat? It depends on which results you mean. Certainly sd can lead to artificial dynamics, but stochastic velocity rescaling can lead to inhomogeneous temperature distribution throughout the system.
> > -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 votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > 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 votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at http://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
