[X] Hi Justin,
Thanks for the reply, and this is the graph, the red curve is what GROMACS gives, the blue curve is what I get.. yes I am considering the unsaturated carbons in to account. I have to see which is closer to the experimental result. Hi Chris, Thanks for the information , I will surely try the VMD tcl script and compute the order parameters and compare. If there is anything else that you suggest kindly let me know , it will be very helpful for me. Thanks again Ramya ________________________________________ 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 here: http://www.gromacs.org/Support/Mailing_Lists#Mailing_List_Etiquette 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. -Justin From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of chris.ne...@utoronto.ca [chris.ne...@utoronto.ca] Sent: Thursday, September 01, 2011 1:35 PM To: gmx-users@gromacs.org Subject: [gmx-users] order parameter In addition to Justin's comment about g_order being incorrect for unsaturated carbons, you won't ever get numerical agreement with g_order, even for saturated carbons, because g_order does not use your explicit hydrogens. g_order uses the positions of the carbons to rebuild the hydrogen positions assuming perfect tetrahedral geometry, which you certainly don't have in all cases when you use real hydrogens. There is a VMD tcl script that you can download that will compute order parameters from real hydrogen atoms. perhaps you should try to compare to that. Chris. -- original message -- 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-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. 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
