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For context, I ran several simulations inside a loop, varying mass composition to see the energy spectrum at the Earth. I noticed that the RAM consumption was exceedingly high after some time. Further…
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Hi everyone,
I'm conducting Solvation Free Energy calculations using QCG for several macromolecules in 100 solvent molecules. I'm curious if it's feasible to employ the GFN-FF method for the Final Ge…
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We are currently working on obtaining free energy information for a large protein complex using a coarse-grained Martini model in OpenMM. However, we've encountered challenges in aligning our calculat…
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Here is the run I am trying to replicate. Below, are the inputs: the two sample sequences, and using DNA parameters.
![image](https://github.com/ViennaRNA/ViennaRNA/assets/124276755/d49417a6-734c-4…
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Dear all,
I am using eABF free energy method to calculate dimerization energy. For this I have divided the 1d CV space in different windows and did the simulations. Now I am having .czar.grad files a…
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Hi, I am trying to run GMT on EC2 Ubuntu 24.0 (since I only have a windows laptop). Is that possible? Also I have some questions about the setup.
1. Do I need to run the application I want to meas…
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We start with #474 to use a different theme. This allows very easy way to write docs in markdown (is also currently supported but doesn't format as nicely).
Todos:
- [ ] Move the dataset module …
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**Is your feature request related to a problem? Please describe.**
If a vehicle, for example an E-scooter, was to be rented it was possible for this vehicle to have had not enough remaining power t…
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When propagating the error for the fitted spectrum, there is an error if the source position is free in the fit (see PR [#78](https://github.com/cositools/cosipy/pull/78)).
We define `results_err =…
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Dear, I am performing the PMF calculation using the ABF method (classic) and tempered metadynamics, but the PMF I obtain are totally different. I am using the distance between monomers of my protein a…