Hi
Thanks for your help with this. The problem was that the size of my 3d grid was too small (I was just using the default 1x1x1 nm). I have now used a grid size that matches my system and have a sensible gro file. Best wishes, -Syma _____ From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Qiao Baofu Sent: 30 March 2007 08:19 To: Discussion list for GROMACS users Subject: Re: [gmx-users] g_sdf again 2007/3/29, Dallas B. Warren <[EMAIL PROTECTED]>: Syma, > I am using g_sdf to calculating the spatial distribution of > lipid headgroups around other species in my system. > > The thing is when I get the gro file (produced by using the -r flag in > g_sdf) and then look at this in vmd or chimera with my > spatial density file (plt), the reference gro file is not > positioned 'in' the box of density produced by g_sdf. > > Is this as it should be and I am interpreting my results > incorrectly, or have I set up my coordinate system incorrectly? That does sound a bit unusual. However, I use g_sdf quite extensively but don't use the reference structure function. Reason for this, is I have found that the one generated for the molecules I simulate it is highly distorted and the corresponding atom locations do not match up with where they they are located if you calculate the sdf for the non-coordinate atoms within the molecule. Yes. I also found that. Because I want to use the COM of the reference group to calculate the sdf, and the problem of "-r" flag, I rewrite this program. It works. But it seems my program always uses too much memory. Who can give some suggestions to save the memory? Thanks a lot! So I use a representative molecule, rotate to match the sdf for atoms within the molecule, then use that. Not the best way to do it, but it gets what I need. Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacology Victorian College of Pharmacy, Monash University 381 Royal Parade, Parkville VIC 3010 [EMAIL PROTECTED] +61 3 9903 9524 --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Sincerely yours, ********************************************** Baofu Qiao, PhD Frankfurt Institute for Advanced Studies Max-von-Laue-Str. 1 60438 Frankfurt am Main, Germany TEL:+49-69-7984-7529 **********************************************
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