[gmx-users] Order Parameter with an all-atom force field

Mohsen Ramezanpour ramezanpour.mohsen at gmail.com
Wed Nov 30 01:51:02 CET 2016

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.


*Rewards work better than punishment ...*

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