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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I have sent this email to the gromacs users emailing list.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I don’t actually use g_spatial as it doesn’t do what I want it to, I use the older g_sdf script. So can’t comment on the output or really help you with it.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">What you are doing seems right from a quick look through. From what you have told the script to so, it seems like it has done exactly what you asked it to.
But without seeing what the system looks like, how it behaves etc, can’t say anything beyond that.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">When I don’t see what I expect, I start with a very simple example, ensure that I what I expect there, then make things gradually more complex. That way you
can work out if you are using the script incorrectly or what you expected to see is actually incorrect.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Catch ya,<br>
<br>
Dr. Dallas Warren<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Medicinal Chemistry and Drug Action<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Monash Institute of Pharmaceutical Sciences</span><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">, Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
dallas.warren@monash.edu<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">+61 3 9903 9304<br>
---------------------------------<br>
When the only tool you own is a hammer, every problem begins to resemble a nail.</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">
<o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> Ianatul Khoiroh [mailto:ianatul_khoiroh@yahoo.com]
<br>
<b>Sent:</b> Friday, 27 April 2012 6:14 PM<br>
<b>To:</b> Dallas Warren<br>
<b>Subject:</b> ask about SDF<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="color:black">Dear Dr. Dallas Warren,<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="color:black">I am sorry for sending you a personal e-mail. FYI, I got your email address from gmx-user mailing list.<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="color:black">I am new to Gromacs and I did little stuff already in it for the last two months. Briefly, my system consist of 10 oligomers + 990 of solvents in cubic box. I did 15 ns NPT equilibration
and currently I am doing analysis stuff such as RDF, density, viscosity, etc. And now I want to try using g_spatial but I stuck on it. I would like to know if you can help me in this.<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="color:black"><br>
In Gromacs 4.5.4 manual, they wrote like this:<br>
<br>
</span><span style="color:#00007F">1. Use make_ndx to create a group containing the atoms around which you want the SDF<br>
2. trjconv -s a.tpr -f a.xtc -o b.xtc -center tric -ur compact -pbc none<br>
3. trjconv -s a.tpr -f b.xtc -o c.xtc -fit rot+trans<br>
4. run g_spatial on the .xtc output of step #3.<br>
5. Load grid.cube into VMD and view as an isosurface</span><span style="color:black"><br>
<br>
I have tried to follow those steps but I coud not get any pretty SDF picture like those I read in many papers. :D<br>
This is what I have done following the above mentioned steps:<br>
</span><span style="color:#C00000">step 1:</span><span style="color:black"> I have my index file<br>
</span><span style="color:#C00000">step 2:</span><span style="color:black"> I choose my oligomers ("solute", 10 oligomers) as group for centering and I select "system" (10 oligomers + 990 solvents) as an output group<br>
</span><span style="color:#C00000">step 3:</span><span style="color:black"> Again, I choose "solute" and choose "system" as an output<br>
</span><span style="color:#C00000">step 4:</span><span style="color:black"> I run g_spatial and select "990 solvents" for both calculation and output. It gives me warning to increase nab values, so I increase the nab = 100. I got grid.cube but the size of the
file is not that big (the manual says it is around 3 copies of *.xtc file). <br>
</span><span style="color:#C00000">step 5:</span><span style="color:black"> I load grid.cube into VMD as an isosurface. I got only a sphere of solvents there on the VMD display<br>
<br>
I would like to know if you could tell me what principally have I did wrong here.... I run Gromacs 4.5.5 in Cygwin.<br>
<br>
I really appreciate your help......Thank you very much.<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:#00007F">Regards,
<br>
<br>
Ianatul Khoiroh<br>
Thermophysical Properties Lab. E2-504<br>
Dept. of Chemical Engineering<br>
National Taiwan University of Science and Technology (NTUST)</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:#00007F">#43 Keelung Road, Sec. 4, Taipei 106, Taiwan R.O.C</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:#00007F">Phone: +886-2-2733-3141 #7605 <br>
E-mail: <a href="mailto:ianatul_khoiroh@yahoo.com">ianatul_khoiroh@yahoo.com</a></span><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#00007F">
</span><span style="color:black"><o:p></o:p></span></p>
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