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):
For CHARMM36:
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.
Cheers
Tom
Igor Marques wrote:
thomas,
i've recently placed a similar question and justin asked me to show my
index for the double bound calculation, so, i'm asking you the same.
you should have
Ci-1
Ci - the first carbon of the double bound
Ci+1 - the second carbon of the double bound
Ci+2
in that index
doing this, for C9 and C10 i've obtained the following values
0.0738068
-0.000533683
that you should then replace in the correct positions in the sn2 output
good luck,
and sorry if i'm missing the point :|
igor
Igor Marques
On Wed, Jun 8, 2011 at 5:53 PM, Thomas Piggot <t.pig...@soton.ac.uk
<mailto:t.pig...@soton.ac.uk>> wrote:
Hi Everyone,
I am facing a problem when calculating the lipid deuterium order
parameters for the unsaturated carbons of the sn-2 tail of POPC
using g_order with GROMACS version 4.5.4 (although I have tried
other older versions too but they all give the same results).
Firstly, I should say the the calculation of the order parameters
for the saturated sn-1 chain (and also both chains of DPPC) behave
as I would expect, and produce order parameters that compare well to
previously published simulations and experimental values.
To calculate the order parameters of the unsaturated chain I am
following the approach as given on the GROMACS website
(http://www.gromacs.org/Documentation/Gromacs_Utilities/g_order), so
splitting the calculation into two parts for the saturated and
unsaturated regions of the chain. The problem I am facing is that
the order parameter for carbon 9 (so the first carbon in the double
bond), calculated using the -unsat option, is much larger than
expected. By this I mean that for the two different force fields I
have tested (namely the CHARMM36 parameters of Klauda et al., and
the GROMOS 53A6L parameters of Poger et al.) the order parameter for
this carbon is much larger than the published simulation values and
also much larger than experimental values. To highlight this, I have
just put the numbers I have obtained using g_order for this carbon
below, and compared to some rough values I have estimated from
figures provided in the Klauda and Poger papers:
CHARMM36
g_order: 0.133732
Klauda estimate: 0.06
GROMOS53A6L:
g_order: 0.199651
Poger estimate: 0.07
Myself and a colleague have tried looking into the code to determine
how the order parameters are calculated using the -unsat option,
however we couldn't quite follow the calculation. Hopefully someone
who knows something more about g_order can help with this problem.
Again I should stress that it appears that the main difference in
order parameters between what I have calculated and the published
ones is just in this one carbon, for both force fields. A similar
issue to this has also been reported previously on the list for this
carbon of POPC using the 'Berger' force field
(http://lists.gromacs.org/pipermail/gmx-users/2010-February/049072.html).
Thank you for any help anyone can give
Cheers
Tom
--
Dr Thomas Piggot
University of Southampton, UK.
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