[gmx-users] Calculation of unsaturated deuterium order parameters for POPC

[Thomas Piggot]

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.piggot at soton.ac.uk 
> <mailto:t.piggot at 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 at gromacs.org
>     <mailto:gmx-users at 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-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> 

-- 
Dr Thomas Piggot
University of Southampton, UK.