On 11/29/16 7:50 PM, Mohsen Ramezanpour wrote:
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., RĂ©at, 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?

Yes. Order parameters are calculated from the positions of the carbon atoms, which is why you can't get terminal values.

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.


They probably used different analysis software and different methods.

-Justin

Thanks in advance for your comments.

Cheers
Mohsen






--
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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