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Questions tagged [packmol]

Questions about (or related to) the PACKMOL software.

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2 votes
0 answers
25 views

Creating 1M NaCl solution using PACKMOL

I want to create a 1M NaCl solution in a 1nm X 1nm X 1nm size cell using PACKMOL. So, what should be the NaCl:H2O ratio for this concentration? My calculation is - 1M NaCl = 1 mole NaCl + 1000 mL H2O =...
Abdullah Shahriar's user avatar
2 votes
0 answers
68 views

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 ...
Hemanth Haridas's user avatar
4 votes
0 answers
42 views

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 ...
Abdul Rauf Kaunda's user avatar
4 votes
1 answer
230 views

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 ...
user6363's user avatar
6 votes
1 answer
292 views

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: ...
SaiSmaran S B PES1201701189PES's user avatar