Dear Gromacs users, I have a question on S_cd order parameters:
Using g_order for a lipid like DSPC, I can get the values for C2 to C17, although DS tail has 18 carbons. I know the reason when I use a united atom force field like Gromos54A7. This is mainly based on the algorithm which it works for united atom. However, when I use Charmm36FF, the algorithm for calculation of S_cd change (based on following article): *Vermeer, L. S., De Groot, B. L., Réat, V., Milon, A., & Czaplicki, J. (2007). Acyl chain order parameter profiles in phospholipid bilayers: computation from molecular dynamics simulations and comparison with 2H NMR experiments. European Biophysics Journal, 36(8), 919-931.* I was wondering if g-order will use the same algorithm which it use for uited atom for all atom too? If NO, how can one tell g_order to use another algorithm which match the all atom force field? Besides, in some articles done by NAMD, I have seen authors have reported values for C18 too when used Charmm36FF. Thanks in advance for your comments. Cheers Mohsen -- *Rewards work better than punishment ...* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
