On 10/3/13 11:50 AM, sa wrote:
Hi all,
I am trying to compute the order parameters for the sn1 and sn2 chains of
DOPC (CHARMM36) in bilayer . I am using the g_order tool (v4.6.3).
I have constructed for each DOPC chain two index files that contains in
the first one all the Carbon atoms where the first Carbon is C=O and the
last one is the last methyl. The second index file for the unsat
calculations contains only the carbons of the C-C9=C10-C.
I am confused here, since the file obtained from g_order w/o the -unsat
argument contains only 16 values and in case of the file generated with
g_order w the -unsat argument 2 values. I am aware that I need to replace
the 9 -10 values in first by those of the second file. However I would like
Remember to renumber the first file so it starts with carbon 2, then make the
replacements.
to compare my SCD values with those obtained by Jämbeck and P. Lyubartsev
(figure 2 in ref [1] ), The authors present graph for DOPC with 17 values.
How it is possible? Did I miss something, here?
I would suggest you contact the authors directly. I see the same thing
frequently from other groups that have used Gromacs, but I cannot ever get the
same outcome, which seems to indicate to me that they are using a modified
version of g_order or they are somehow extrapolating their values. In any case,
if you figure out how they're doing it, please report back because this is a FAQ
on this list when it comes to lipid analysis.
-Justin
-- g_order w/o unsat
# g_order_mpi is part of G R O M A C S:
#
# GROup of MAchos and Cynical Suckers
#
@ title "Deuterium order parameters"
@ xaxis label "Atom"
@ yaxis label "Scd"
@TYPE xy
1 0.20508
2 0.148241
3 0.184247
4 0.184565
5 0.184457
6 0.166101
7 0.118359
8 0.0774722
9 0.0703466
10 0.0511651
11 0.0977673
12 0.0968413
13 0.100903
14 0.0869513
15 0.0806322
16 0.0602708
-- g_order w/ unsat
# g_order_mpi is part of G R O M A C S:
#
# GRoups of Organic Molecules in ACtion for Science
#
@ title "Deuterium order parameters"
@ xaxis label "Atom"
@ yaxis label "Scd"
@TYPE xy
1 0.104554
2 0.0111027
[1] http://pubs.acs.org/doi/full/10.1021/ct300342n
Thank in advance
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==================================================
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