Hello,<br><br>I intend to generate a stack of molecules with the command line:<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="border: medium none ; padding: 0in; text-align: justify;">genconf
-f Hexane.gro -nbox 8 6 4 -o Hexane-STACK.gro</p>
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<br>Hexane.gro has box size of 3*3*3 nm3 and I need to have about 7 molecules per nm^3. So I multiplied 7 by 27 (box size) to get (7*27=)189 molecuels. What I get from the above command is (-nbox 8 6 4 )192 but the system size in getting bigger as well!. <b> 24.00000 18.00000 12.00000 nm^3.</b> <br>
<br>Could you dear experts guide me how I can reach the system density I want. Also to I wanted to know what is best value -dist option. Is it ok if I leave the distance between boxes 0 0 0?<br><br>Thank you, <br> <br>Hexane-STACK.gro:<br>
<br>Glycine aRginine prOline Methionine Alanine Cystine Serine<br> 3840<br> 1HEX C1 1 1.786 1.639 1.501 0.0000 0.0000 0.0000<br> 1HEX H11 2 1.881 1.608 1.500 0.0000 0.0000 0.0000<br> 1HEX H12 3 1.768 1.696 1.421 0.0000 0.0000 0.0000<br>
1HEX H13 4 1.770 1.692 1.584 0.0000 0.0000 0.0000<br> 1HEX C2 5 1.693 1.518 1.499 0.0000 0.0000 0.0000<br> 1HEX H21 6 1.711 1.461 1.579 0.0000 0.0000 0.0000<br> 1HEX H22 7 1.710 1.465 1.416 0.0000 0.0000 0.0000<br>
1HEX C3 8 1.547 1.561 1.501 0.0000 0.0000 0.0000<br> 1HEX H31 9 1.528 1.617 1.420 0.0000 0.0000 0.0000<br> 1HEX H32 10 1.530 1.615 1.584 0.0000 0.0000 0.0000<br> 1HEX C4 11 1.454 1.440 1.500 0.0000 0.0000 0.0000<br>
1HEX H41 12 1.472 1.384 1.581 0.0000 0.0000 0.0000<br> 1HEX H42 13 1.472 1.386 1.418 0.0000 0.0000 0.0000<br> 1HEX C5 14 1.307 1.483 1.501 0.0000 0.0000 0.0000<br> 1HEX H51 15 1.289 1.539 1.420 0.0000 0.0000 0.0000<br>
1HEX H52 16 1.289 1.537 1.583 0.0000 0.0000 0.0000<br> 1HEX C6 17 1.214 1.361 1.500 0.0000 0.0000 0.0000<br> 1HEX H61 18 1.119 1.392 1.501 0.0000 0.0000 0.0000<br> 1HEX H62 19 1.231 1.307 1.418 0.0000 0.0000 0.0000<br>
1HEX H63 20 1.232 1.305 1.581 0.0000 0.0000 0.0000<br> 2HEX C1 21 1.786 1.639 4.501 0.0000 0.0000 0.0000<br> 2HEX H11 22 1.881 1.608 4.500 0.0000 0.0000 0.0000<br> 2HEX H12 23 1.768 1.696 4.421 0.0000 0.0000 0.0000<br>
2HEX H13 24 1.770 1.692 4.584 0.0000 0.0000 0.0000<br> 2HEX C2 25 1.693 1.518 4.499 0.0000 0.0000 0.0000<br> 2HEX H21 26 1.711 1.461 4.579 0.0000 0.0000 0.0000<br> 2HEX H22 27 1.710 1.465 4.416 0.0000 0.0000 0.0000<br>
2HEX C3 28 1.547 1.561 4.501 0.0000 0.0000 0.0000<br> 2HEX H31 29 1.528 1.617 4.420 0.0000 0.0000 0.0000<br> 2HEX H32 30 1.530 1.615 4.584 0.0000 0.0000 0.0000<br> 2HEX C4 31 1.454 1.440 4.500 0.0000 0.0000 0.0000<br>
2HEX H41 32 1.472 1.384 4.581 0.0000 0.0000 0.0000<br> 2HEX H42 33 1.472 1.386 4.418 0.0000 0.0000 0.0000<br> 2HEX C5 34 1.307 1.483 4.501 0.0000 0.0000 0.0000<br> 2HEX H51 35 1.289 1.539 4.420 0.0000 0.0000 0.0000<br>
2HEX H52 36 1.289 1.537 4.583 0.0000 0.0000 0.0000<br>.<br>.<br>.<br>.<br>.<br>192HEX C1 3821 22.786 16.639 10.501 0.0000 0.0000 0.0000<br> 192HEX H11 3822 22.881 16.608 10.500 0.0000 0.0000 0.0000<br>
192HEX H12 3823 22.768 16.696 10.421 0.0000 0.0000 0.0000<br> 192HEX H13 3824 22.770 16.692 10.584 0.0000 0.0000 0.0000<br> 192HEX C2 3825 22.693 16.518 10.499 0.0000 0.0000 0.0000<br> 192HEX H21 3826 22.711 16.461 10.579 0.0000 0.0000 0.0000<br>
192HEX H22 3827 22.710 16.465 10.416 0.0000 0.0000 0.0000<br> 192HEX C3 3828 22.547 16.561 10.501 0.0000 0.0000 0.0000<br> 192HEX H31 3829 22.528 16.617 10.420 0.0000 0.0000 0.0000<br> 192HEX H32 3830 22.530 16.615 10.584 0.0000 0.0000 0.0000<br>
192HEX C4 3831 22.454 16.440 10.500 0.0000 0.0000 0.0000<br> 192HEX H41 3832 22.472 16.384 10.581 0.0000 0.0000 0.0000<br> 192HEX H42 3833 22.472 16.386 10.418 0.0000 0.0000 0.0000<br> 192HEX C5 3834 22.307 16.483 10.501 0.0000 0.0000 0.0000<br>
192HEX H51 3835 22.289 16.539 10.420 0.0000 0.0000 0.0000<br> 192HEX H52 3836 22.289 16.537 10.583 0.0000 0.0000 0.0000<br> 192HEX C6 3837 22.214 16.361 10.500 0.0000 0.0000 0.0000<br> 192HEX H61 3838 22.119 16.392 10.501 0.0000 0.0000 0.0000<br>
192HEX H62 3839 22.231 16.307 10.418 0.0000 0.0000 0.0000<br> 192HEX H63 3840 22.232 16.305 10.581 0.0000 0.0000 0.0000<br> <b> 24.00000 18.00000 12.00000</b><br><br><br><br>*******************Hexane.gro<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<br>
> 0.00000 0.00000<input id="gwProxy" type="hidden"><input onclick="jsCall();" id="jsProxy" type="hidden"><div id="refHTML"></div>