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<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Hi </span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'> </span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Thanks for your help with this.</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'> </span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>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.</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'> </span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Best wishes,</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'> </span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>-Syma</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'> </span></font></p>
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<p class=MsoNormal><b><font size=2 face=Tahoma><span lang=EN-US
style='font-size:10.0pt;font-family:Tahoma;font-weight:bold'>From:</span></font></b><font
size=2 face=Tahoma><span lang=EN-US style='font-size:10.0pt;font-family:Tahoma'>
gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org] <b><span
style='font-weight:bold'>On Behalf Of </span></b>Qiao Baofu<br>
<b><span style='font-weight:bold'>Sent:</span></b> 30 March 2007 08:19<br>
<b><span style='font-weight:bold'>To:</span></b> Discussion list for GROMACS
users<br>
<b><span style='font-weight:bold'>Subject:</span></b> Re: [gmx-users] g_sdf
again</span></font></p>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'> </span></font></p>
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face="Times New Roman"><span style='font-size:12.0pt'> </span></font></p>
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<p class=MsoNormal><span class=gmailquote><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>2007/3/29, Dallas B. Warren <<a
href="mailto:Dallas.Warren@vcp.monash.edu.au">Dallas.Warren@vcp.monash.edu.au</a>>:</span></font></span></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>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. </span></font></p>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><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>
</span></font></p>
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<blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;
margin-left:4.8pt;margin-right:0cm'>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'> </span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>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>
a nail.<br>
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<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><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 <br>
********************************************** </span></font></p>
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