[gmx-users] order parameter
Justin A. Lemkul
jalemkul at vt.edu
Thu Sep 1 18:59:55 CEST 2011
Parthasarathi, Ramya wrote:
> Thanks lot for replying. I am doing all-atom simulation. I am doing the PBC before finding the angle. also I normalise the vectors before finding the angle.
> Yes I have checked that the formula I am using for the order parameter is correct.
> I am doing the averaging correctly.
> 1. I take the carbons in each tail ( I neglect the 1st and the last as GROMACS does) , then I find the Hydrogens associated with it.
> 2. Then I do the PBC , normalise them and then take the angle, then calculate the order parameter.
> 3. finally I average them over the frames.
> I have gone through the procedure and still I am not getting the same profile as GROMACS gives.
> Is there anything else that I need to include in my calculations?
There are several additional points to consider.
1. What type of differences are you getting? An image would be nice to see,
otherwise no one has any chance of knowing what's going on. See point number 4
2. Which results are more accurate with respect to experimental results, yours
or those produced by g_order?
3. Are you analyzing saturated or unsaturated chains? There is a known problem
with g_order's ability to calculated order parameters for unsaturated carbons,
although I'm not sure if it's been filed on redmine yet. It's been discussed a
number of times.
> From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of chris.neale at utoronto.ca [chris.neale at utoronto.ca]
> Sent: Wednesday, August 31, 2011 8:00 PM
> To: gmx-users at gromacs.org
> Subject: [gmx-users] order parameter
> Dear Ramya:
> Are you simulating all-atom lipids (with explicit hydrogen atoms on
> the acyl chain)? If not, then you missed a step in your description of
> what you have done (g_order, for example, ignores explicit hydrogen
> atoms so that it can act on united atom lipids).
> Not sure why PBC would be your step #3, after your step #2 was to find
> the angle. I suggest that you simply run trjconv -pbc mol on your
> trajectory file before you process it and then you no longer need to
> worry about PBC in your custom analysis tool.
> Once you have the angle, you must average it correctly. The equation
> is available in most papers that describe order parameters and is
> listed as a comment at the top of the gmx_order.c source file (in
> version 4.0.7 at least).
> If you want to get more help on your procedure after you have worked
> on this for a while, I suggest laying out your procedure very
> specifically. Your previous post, for example, was pretty loose with
> terminology when you described your method and there is quite a bit
> that one must assume.
> -- original message --
> I am trying to write a code for Deuterium order parameter of DOPC
> lipid. I went through the code in gmx_order.c, I did the following,
> 1. I took the carbons in the chain, and found its neighbors.
> 2. Took the bilayer normal and found the angle between the
> bilayer normal and the ?CH molecular axis.
> 3. Took care of the periodic boundary conditions since I use NPT
> But the code in gmx_order.c in GROMACS tries to do a lot of things
> other than this, as I don?t know C or C++ language that it is using, I
> don?t know what else I am supposed to include.
> Can someone please help me?
> gmx-users mailing list gmx-users at gromacs.org
> 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.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users