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NB. I assigned CR to this one, because I'm focussing on temperature scales now. I think it's just a matter of 10 minutes of web searching, to find an answer...
In working on #1293, which relates to…
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After running several iterations, we found that some of the states potential energies went up to very high values. I tried YANK simulations with Langevin integrator and simulations with Hamiltonian Mo…
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Pymbar cannot be installed from pypi because `pymbar/_pymbar.c` is missing from the tarball.
I try to install pymbar on python 2.7 in a fresh virtualenv:
```bash
mkvirtualenv pymbar-test -p pyt…
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This relates to https://github.com/WCRP-CMIP/CMIP6_CVs/issues/312 and https://github.com/cmip6dr/CMIP6_DataRequest_VariableDefinitions/issues/85. People want to provide river flow information on the g…
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I'm doing some dTRAM analysis and I have the following problem:
If I run
dtram(... , lag=20,...)
or
dtram(... , lag=[5,10,20], ...)
(with exactly all the others parameters/input variables, un…
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It's going to really slow down our ability to debug YANK (as well as throughput even for fast calculations) if the startup time is so absurdly long.
I suggest we use some sort of timing/logging fac…
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**Reported by johan_ylikiiskila on 5 Nov 2015 15:25 UTC**
The Pipes.DynamicPipe component has two parameters used for initializing pressure _p_a_start_ and _p_b_start_. These are propagated to all sta…
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I have a pretty small system (48. 20. 34. A as the box dimensions). So the error that I am getting is:
```
File "/root/anaconda2/envs/rezayank/lib/python2.7/site-packages/simtk/openmm/openmm.py"…
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Dear Mr. Otis and Mr. Bocklund,
Is metastability in anyway integrated in this module? I mean: is it possible to plot phase diagrams with metastable phases and to study thermodynamic properties of m…
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Hi all,
I have been running Tram on a set of biased and unbiased simulation data, and I argue the results are not converging but I cannot figure out why.
I have a set of 24 umbrella sampling simulati…