[gmx-users] order parameter of small molecule

[manoj gadhwal]

Dear friends,
I have done MD simulation for a small molecule in DPPC bilayer and plain
DPPC.
I have calculated the deuterium order parameters SCD by option g_order for
acyl chain. I have prepared the index file. On comparison with plain DPPC
order parameters, the values for acyl chain of DPPC bilayer when small
molecule in DPPC, the SCD values are fluctuating from positive to negative.
but with plain DPPC the order parameter are appropriate as described in
literature (all positive values).
What can be the possible reason for the negative values coming for
Deuterium order parameters?
Please help....



This is the command used for determining order parameters.
g_order -f dppc_traj.xtc -s dppc_md.tpr -n sn1.ndx -o dppc_md.order_sn1.xvg
-od dppc_md_deuter_sn1.xvg -ob dppc_md_20ns_eiwit.pdb -os
dppc_md_20ns_sliced.xvg -d z

-- 
Manoj Kumar Gadhwal,
PhD Scholar,
Prin. K. M. Kundnani College of Pharmacy,
Colaba, Mumbai-05.
Cont. No. +91 9769051866