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Force field conformer jobs of prenol, 2,3-dimethylbut-2-ene and their radicals, RO2, RO2H, OOQOOH indicates they could possess free CH3 rotors in MMFF94s. Here, I provide an example of prenol.
2D str…
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Hi @tkoziara,
Would it be possible to include functionality to model a spherical joint (ball in socket) with rotational stiffness. Specifically we are intending to translate the LS-DYNA keywords *…
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I use parmEd to build AMBER topologies from GROMACS files(in charmm ff), it worked perfectly for normal proteins, but my protein has non-natural amino acid in it, and it did not work. How to add param…
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Would it be possible to share a link to the research or reasoning behind the `soft_to_angle` Module for someone new to structural protein problems?
My current hunch is that you have run a mixture …
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I just added a short example of COMBINE with PERIODIC in the manual (on Pratyush request).
Better thinking about it, I think we could automatize this choice for COMBINE. I write here how I think we c…
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I'm taking the information from Alford et al's 2017 paper, especially page 3033 and 3034.
A copy is posted at: https://daslab.stanford.edu/site_data/pub_pdf/2017_Alford_JCTC.pdf
The main issues …
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Dear Admin,
May I know whether there is a way to convert MARTINI topology files in Gromacs to run in NAMD? If not, then maybe this can be a feature request?
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These are parameter splits I added based on my [2D k vs equilibrium value dashboard](https://github.com/ntBre/lipoma/blob/master/twod.py). The refitting files can be found [here](https://github.com/nt…
ntBre updated
8 months ago
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While pulling together various disparate forcefields I've occasionally been bitten by missing parameters going unnoticed for some time, causing (for example) particular hydrogens to go floating off. I…
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Up to this point we have used `lambda_electrostatics` to control the interactions rather than the charges, but if we want to keep things consistent we need to address these cases:
- With exact treatm…