Questions tagged [packmol]
Questions about (or related to) the PACKMOL software.
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Creating Monoclinic boxes with Packmol?
I am trying to reproduce this paper and the unit cell for the system is Monoclinic. I have already generated the surface, and now need to generate the waterbox that is placed in contact with the ...
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How to create a water droplet (half-sphere) on a rock (quartz) surface
I am to Equilibrate a uniformly distributed spc water molecules at 300k in 50x50x50 box. Water density is taken to be 1000kg/m3. Simulate the system in the NVT ensemble. The spc water is modeled using ...
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Adding vacuum region in PACKMOL
How do you specify a symmetric vacuum region (along z) above and below an inorganic substrate using PACKMOL? I tried to increase the box size in .pdb and use that in packmol. But it changes the box ...
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Why am I losing bonds when I use PACKMOL on two proteins?
I recently started using PACKMOL to pack a few proteins together. I wrote this PACKMOL code:
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