[gmx-users] Order parameters negative value
t.piggot at soton.ac.uk
Tue Nov 29 23:55:17 CET 2016
To be sure of anything, you need to provide more information.
Deuterium order parameters (which is what I assume you are referring to)
are normally reported as -Scd or |Scd|, so obtaining negative values
from standard analysis tools is perfectly normal. What do you mean by
"not like the commons"? You need to tell us exactly (i.e. copy and paste
from the command line) what you have done to work the order parameters
out and you should also provide the results you have obtained that you
think are incorrect. Information as to the simulation details (e.g.
force field, cut-off's, etc.) will also help too in terms of diagnosing
what is going on.
As for deuterium order parameters in general, yes they can be both
positive and negative whilst still being correct. That said, with fully
saturated tails (as in DPPC/DPPE) you should be seeing (with -Scd) some
pretty normal order parameters plots ranging from about ~0.2/0.25 for
the carbons near the glycerol part of the tails (exact values will
depend upon the simulation temperature and force field used) and then
tailing off (i.e. getting lower) towards the carbons near the ends of
the lipid tails.
On 29/11/16 20:09, Poncho Arvayo Zatarain wrote:
> Hello: I´m analyzing the order parameters of a mixed membrane (25% dppc-75% dppe), but some of the values are negative and the graphic is not like the commons. Is this fine? the values for order parameters can be negative? what means negative values in an order parameters?
Dr Thomas Piggot
University of Southampton, UK.
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