Hi, I am using a united atom forcefield. gromos53a6. So does that mean as long as I avoid the double bond and the subsequent carbons after the double bond, then the calculation is correct? I understand it does not describe the full lipid length but can be used to assess the monolayer behaviour roughly.
Merril. On 10 Mar 2017 12:04 a.m., "Thomas Piggot" <t.pig...@soton.ac.uk> wrote: > The order parameters calculated for all the saturated carbons will be > correct but the gmx order program doesn't calculate the order parameters > for the unsaturated carbons correctly (even when using the -unsat option). > > Out of interest, is this a united-atom or all-atom force field you are > using? > > Cheers > > Tom > > On 09/03/17 23:51, Merril Mathew wrote: > >> Hi, >> >> I followed turorials found on Bevanlab by Justin. I successfully >> calculated >> order parameter for DPPC molecules in my system following the tutorial. My >> question is whether the same calculation can be applied for a POPG >> molecule >> with a double bond in the acyl chain.? can I group all the carbon upto the >> double bond, therefore ignoring the double bond and the rest of the >> carbons >> in the chain to calculate order parameter? Is that a reasonable analysis >> to >> measure the order of POPG molecules.? Thanks. >> > > -- > Dr Thomas Piggot > Visiting Fellow > University of Southampton, UK. > > -- > 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.