Do you have the same amount of molecules in each simulation? Anders
On Fri, Jan 13, 2017 at 12:19 PM, Albert <mailmd2...@gmail.com> wrote: > Hi Mark. > > thanks a lot for your comments. > > These two peptides are isomers. > > I want to know which conformations is more favourable than the other from > the aspect of potential energy..... > > However, the system potential energy and the peptide potential energy > seems to be inconsistent with each other.... So I am pretty confused right > now.... > > regards > > > > On 01/13/2017 12:16 PM, Mark Abraham wrote: > >> Hi, >> >> Having low potential energy (whether in dynamical simulation or em) and >> being (any kind of) stable are nearly unrelated concepts. There may be a >> way to measure what you want, but so far I suspect you haven't worked out >> a >> good way to describe what you want. >> >> Further, unless your peptides are isomers, your potential energies are of >> systems with different composition, so can't be compared. >> >> Mark >> > > > -- > 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. > -- 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.