[gmx-users] Order parameters negative value

[Thomas Piggot]

Hi,

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.

Cheers

Tom

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
Visiting Fellow
University of Southampton, UK.