Hi Gromacs user community a) I was wondering if it is possible to mix a common pair of PCs from two simulations (say, PC1 from a bound simulation vs PC1 from unbound simulation or for that matter wild vs mutant) as an reaction coordinates to generate a comparative reduced free energy profile using the g_sham utility.
b) Will such a approach generate a meaningful comparative free energy plot, akin to an conformational landscape plot commonly generated by plotting PC1 of one system vs. PC1 another system, to highlight the difference /overlap in the conformational sub-space sampled by the two systems c) Given my understanding of underlying formula ∆G(R) = -*KBT *[ln P(R) – ln P(max)] as implemented in g_sham i presume that it is impossible, since mixing of PCs from two different systems will not ensure a proper probability distribution, the data points has to be similar. Thanking in advance Regards, Vijayan.R -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
