Hi, 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? Ramya ________________________________________ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of chris.ne...@utoronto.ca [chris.ne...@utoronto.ca] Sent: Wednesday, August 31, 2011 8:00 PM To: gmx-users@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. Chris. -- original message -- Hi, 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 ensemble. 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? Ramya -- 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