Dear gmx users,<br><br>I tried to generate a stack of molecules using<br><br><meta http-equiv="Content-Type" content="text/html; charset=utf-8"><meta name="ProgId" content="Word.Document"><meta name="Generator" content="Microsoft Word 11"><meta name="Originator" content="Microsoft Word 11"><link rel="File-List" href="file:///C:%5CDOCUME%7E1%5Cmoeed%5CLOCALS%7E1%5CTemp%5Cmsohtml1%5C01%5Cclip_filelist.xml"><style>
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<p class="PreformattedText" style="text-align: justify;"><b><span style="">genconf_d -f Hexane.gro -nbox 4.0 8.0 8.0 -dist 1.1 0.55 0.55 -o
Hexane-stack.gro</span></b></p><p class="PreformattedText" style="text-align: justify;"><br></p><p class="PreformattedText" style="text-align: justify;">I ran the MD simulation successfully but now I want to change the number of molecules so that I get the desired system density. To do so I played a bit with -dist and -box options but I find it not easy to reach desired density. I need to have nearly 7 molecules per nm^3. </p>
<p class="PreformattedText" style="text-align: justify;"><br></p><p class="PreformattedText" style="text-align: justify;">Regarding genbox program in the literature I see that it is recommended for solvation of a solute in water. (The reason I want to try this is because it seems I can directly enter the number of molecules with -nmol option)<br>
</p><p class="PreformattedText" style="text-align: justify;"><br></p><p class="PreformattedText" style="text-align: justify;"><br></p><p class="PreformattedText" style="text-align: justify;">1-I am sorry for asking ridiculous questions but does it make sense if I use genbox and I ask the program solvate a single hexane molecule with hexane molecules?<br>
</p><p class="PreformattedText" style="text-align: justify;">genbox –cp Hexane.gro –cs HExane.gro –p Hexane.top –o solvated.pdb <br></p><p class="PreformattedText" style="text-align: justify;"><br></p><p class="PreformattedText" style="text-align: justify;">
(although this command line is not working I want to know if there is any way to modify the command to get it working or my idea is totally wrong!)<br></p><p class="PreformattedText" style="text-align: justify;"><br></p><p class="PreformattedText" style="text-align: justify;">
2- Initialiy one single hexane molecule is in a box of 3*3*3 nm^3 (Hexane.gro). What is the best approach for doing such calculations. Can I take any arbitrary box size and then based on the box size put a specific No. of particles in it so that I get density?<br>
</p><p class="PreformattedText" style="text-align: justify;"><br></p><p class="PreformattedText" style="text-align: justify;">Thank you,<br></p><p class="PreformattedText" style="text-align: justify;"><br></p><p class="PreformattedText" style="text-align: justify;">
<br></p><p class="PreformattedText" style="text-align: justify;"><br></p><p class="PreformattedText" style="text-align: justify;">Hexane.gro:</p><p class="PreformattedText" style="text-align: justify;"><br><b><span style=""></span></b></p>
Glycine aRginine prOline Methionine Alanine Cystine Serine<br> 20<br> 1HEX C1 1 1.786 1.639 1.501<br> 1HEX H11 2 1.881 1.608 1.500<br> 1HEX H12 3 1.768 1.696 1.421<br> 1HEX H13 4 1.770 1.692 1.584<br>
1HEX C2 5 1.693 1.518 1.499<br> 1HEX H21 6 1.711 1.461 1.579<br> 1HEX H22 7 1.710 1.465 1.416<br> 1HEX C3 8 1.547 1.561 1.501<br> 1HEX H31 9 1.528 1.617 1.420<br>
1HEX H32 10 1.530 1.615 1.584<br> 1HEX C4 11 1.454 1.440 1.500<br> 1HEX H41 12 1.472 1.384 1.581<br> 1HEX H42 13 1.472 1.386 1.418<br> 1HEX C5 14 1.307 1.483 1.501<br>
1HEX H51 15 1.289 1.539 1.420<br> 1HEX H52 16 1.289 1.537 1.583<br> 1HEX C6 17 1.214 1.361 1.500<br> 1HEX H61 18 1.119 1.392 1.501<br> 1HEX H62 19 1.231 1.307 1.418<br>
1HEX H63 20 1.232 1.305 1.581<br> 3.00000 3.00000 3.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000<br><br><input id="gwProxy" type="hidden"><input onclick="jsCall();" id="jsProxy" type="hidden"><div id="refHTML">
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