<br><br><div><span class="gmail_quote">2007/3/29, Dallas B. Warren <<a href="mailto:Dallas.Warren@vcp.monash.edu.au">Dallas.Warren@vcp.monash.edu.au</a>>:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Syma,<br><br>> I am using g_sdf to calculating the spatial distribution of<br>> lipid headgroups around other species in my system.<br>><br>> The thing is when I get the gro file (produced by using the -r flag in
<br>> g_sdf) and then look at this in vmd or chimera with my<br>> spatial density file (plt), the reference gro file is not<br>> positioned 'in' the box of density produced by g_sdf.<br>><br>> Is this as it should be and I am interpreting my results
<br>> incorrectly, or have I set up my coordinate system incorrectly?<br><br>That does sound a bit unusual.<br><br>However, I use g_sdf quite extensively but don't use the reference<br>structure function. Reason for this, is I have found that the one
<br>generated for the molecules I simulate it is highly distorted and the<br>corresponding atom locations do not match up with where they they are<br>located if you calculate the sdf for the non-coordinate atoms within the
<br>molecule. </blockquote><div><br>Yes. I also found that. <br>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!
<br> </div><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">So I use a representative molecule, rotate to match the sdf<br>for atoms within the molecule, then use that. Not the best way to do
<br>it, but it gets what I need.<br><br>Catch ya,<br><br>Dr. Dallas Warren<br>Lecturer<br>Department of Pharmaceutical Biology and Pharmacology<br>Victorian College of Pharmacy, Monash University<br>381 Royal Parade, Parkville VIC 3010
<br><a href="mailto:dallas.warren@vcp.monash.edu.au">dallas.warren@vcp.monash.edu.au</a><br>+61 3 9903 9524<br>---------------------------------<br>When the only tool you own is a hammer, every problem begins to resemble<br>
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</div><br><br clear="all"><br>-- <br>Sincerely yours,<br>**********************************************<br>Baofu Qiao, PhD<br>Frankfurt Institute for Advanced Studies<br>Max-von-Laue-Str. 1<br>60438 Frankfurt am Main, Germany TEL:+49-69-7984-7529
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