Thomas Piggot wrote:
Hi Igor,

Thanks for the reply but I think you slightly missed the point I was trying to make. I followed the approach you mention for the double bond and (with the two force fields I tried) got the values I discussed in my last email, which when compared to the published values seem to be incorrect.

Just to confirm, my index file (for the unsaturated calculation) contains (below is just pasted from make_ndx):


  0 C28                 :    72 atoms
  1 C29                 :    72 atoms
  2 C210                :    72 atoms
  3 C211                :    72 atoms

and for GROMOS53A6L:

  0 C1H                 :   128 atoms
  1 C1I                 :   128 atoms
  2 C1J                 :   128 atoms
  3 C1K                 :   128 atoms

My command for g_order (this is just for CHARMM36 but I use the same command for GROMOS53A6L on different files) is:

g_order_4.5.4 -s for-md-popc-charmm36.tpr -f md-popc-charmm36.xtc -n chain2_unsat.ndx -od deut_chain2_unsat.xvg -unsat

If anyone can see what might be going wrong then any help would be greatly appreciated.

Are your results converged? From the g_order command, you're considering the whole trajectory. I'd suggest the usual block averaging approach to see if you're converged.

There's nothing wrong with the way you're calculating the order parameters, so the only other thing I would suspect (other than lack of convergence) is that the .mdp settings are somehow giving unexpected results. Membrane properties can be very sensitive to vdW and electrostatics methods.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at] | (540) 231-9080

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