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I tried working with working with the clawpack.geoclaw.topotools in the topotools_examples.ipynb and when i tried to plot the topography data using
topo.plot()
I keep getting this following erro…
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Hello @sangramkadam,
Thank you for such an amazing paper!
I'm new to the LAMMPS software. Could you please tell me how to generate the conf.dat file?
I want to build a 3D structure as you sho…
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Hello,
I have been using TopoTools version 1.9 and encountered an issue when using the "topo guessimpropers" command. Specifically, the central atom of the improper (the one with 3 bonds) is not al…
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Dear all,
Thanks for the helpful code. Is there any way to combine all the pdb/psf files after the minimization with namd?
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There is old code in vitess that invokes syslog. This has mostly been problematic:
* Most containers don't have syslog enabled.
* It was known to have caused unnecessary disk I/O.
* No one knows it…
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**Summary**
Add new namespace "elements" with tables/maps and functions accessing them for a variety of mappings related to chemical elements and their properties like atomic number, atomic mass, c…
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A rookie one:
I'm having trouble running the GUI on Matlab 2018b (with all toolboxes required).
Topotoolbox and TAK are on the same folder, in my matlab path.
When trying to run the GUI, this e…
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Hi everyone,
I am trying to generate gmx topologies for my protein, which so far worked great. But I got a bug recently that I could not solve thus far.
I have attached the files that generate t…
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**Expected behavior**
len(Universe.residues) should provide the correct number of residues for the system.
**Actual behavior**
len(U.residues) is incorrect and inconsistent with the supplie…
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HI,
I am new to Moltemplate. I am trying to build a small organic molecule for lammps. I obtained the all_atom_geometry_optimized.lt, In this file it automatically using GROMOS_54A7_ATB which I wan…