Quoting pragya chohan <[EMAIL PROTECTED]>: > > Dear Users > I have a system in of protein with in bound chlorine ion. I also added Na ion > to the system to neutralize charge on system. I have to couple the system to > water bath. can i couple protein chlorine and Na together and solvent > separately? or should i couple protein and chlorine together and solvent and > na together?
You could do either. Try make_ndx -h. But generally, when I simulate a protein in water and ions, I simply couple the whole system to the same bath. See here: http://wiki.gromacs.org/index.php/Thermostats > I the later case -n option would take in 2 index files. then what should I > do? Specify both groups within the same index file. Again, make_ndx -h. Type 'help' for some examples. -Justin > Thanks in advance > _________________________________________________________________ > Tried the new MSN Messenger? ItÂ’s cool! Download now. > http://messenger.msn.com/Download/Default.aspx?mkt=en-in ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
