thomas,<br><br>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.<br>you should have<br><blockquote style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;" class="gmail_quote">
Ci-1<br>Ci - the first carbon of the double bound<br>Ci+1 - the second carbon of the double bound<br>Ci+2<br></blockquote>in that index<br><br>doing this, for C9 and C10 i've obtained the following values<br> 0.0738068<br>
-0.000533683<br><br>that you should then replace in the correct positions in the sn2 output<br><br><br>good luck,<br>and sorry if i'm missing the point :|<br><br><br>igor<br><br><br clear="all"> Igor Marques<br>
<br><br><div class="gmail_quote">On Wed, Jun 8, 2011 at 5:53 PM, Thomas Piggot <span dir="ltr"><<a href="mailto:t.piggot@soton.ac.uk">t.piggot@soton.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Hi Everyone,<br>
<br>
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).<br>
<br>
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.<br>
<br>
To calculate the order parameters of the unsaturated chain I am following the approach as given on the GROMACS website (<a href="http://www.gromacs.org/Documentation/Gromacs_Utilities/g_order" target="_blank">http://www.gromacs.org/Documentation/Gromacs_Utilities/g_order</a>), 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:<br>
<br>
CHARMM36<br>
<br>
g_order: 0.133732 <br>
Klauda estimate: 0.06<br>
<br>
<br>
GROMOS53A6L:<br>
<br>
g_order: 0.199651<br>
Poger estimate: 0.07<br>
<br>
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 (<a href="http://lists.gromacs.org/pipermail/gmx-users/2010-February/049072.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/2010-February/049072.html</a>).<br>
<br>
Thank you for any help anyone can give<br>
<br>
Cheers<br>
<br>
Tom<br>
<br>
-- <br>
Dr Thomas Piggot<br>
University of Southampton, UK.<br><font color="#888888">
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