<div class="gmail_quote">Hey gmx users,<br> I just began studying gmx, here is a basic question irritating me. There is a methanol.pdb ( box size: 23.619 23.619 23.619) in tutor, I want to put a same size water box on the right side of methanol box to simulate the mixing process. I know there is a mix.pdb file in tutor already, but I want to create it by myself. When I use genbox :<br>
genbox -cp methanol.pdb -cs spc216 -o mix.pdb -box 4.7238 2.3619 2.3619<br><br>1. The problem is, in created mix.pdb file, some water molecules always inserted in methanol box. How can I just create a pdb file of left methanol box only contains methanol and right water box only contains water?<br>
<br><br>2. If use "genbox -cs spc216 -o water.pdb -box 2.3619 2.3619 2.3619" to create a water box, how can I get a configuration which the first atom's coordinates are 0 0 0? <br><br>Thanks in advance.<br>
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<br>William<br>
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