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> 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.
> --
> gmx-users mailing list gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
