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Hi guys! Recently I'm using BioSimSpace to minimize and equilibrate perturbable systems before running the main simulation and meet some [problems](https://github.com/michellab/BioSimSpace/issues/222)…
kexul updated
2 years ago
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Hi all,
With the attached files, running "sire_python /path/to/somd-freenrg.py -C Config.cfg" behaves rather oddly. In the output I get
```
=====================================================…
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To add to the roundup todo list, use the following markdown format.
```
- [ ] optional description [link name](/link/to/item)
```
So it generates the following:
- [x] optional description [li…
skial updated
3 years ago
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I am running one-way shooting OPS simulations with Gromacs using the 1.3.0.dev0 version. After a random amount of cyles (could be after 280 Monte Carlo cyles but also after 70) an error occurs and the…
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@Mikhail-Vaganov some comments on the proposal someone gave me:
Periodic Boundary Condition (PBC)
Distance
The student says that for the Periodic Boundary condition appropriate particles copies…
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I am running some simple production MD, and am seeing protein unfolding where there shouldn't be any. This is the code I run:
```python
import BioSimSpace as BSS
from shutil import copyfile
syst…
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I was able to get the 2D wave tank example running in 0.5.1, however, faithfully replicating the case in 0.6.0.1911-07-2 leads to the error below. The case looks fine in ParaView, and the settings for…
kwadl updated
4 years ago
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Hi,
I am a new Gromacs user and came across your package which has the potential to be very useful to me. Unfortunately, I have had problems using MDPOW. I'm pretty sure Gromacs is installed proper…
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My system possess intell i7 2700k with GPU RTX1060
My OS is Linuxmint 19.2 64bit, NVIDIA driver 435 with CUDA 10.1
Installed miniconda3 of python 3.8
it returns error... assuming its a python ve…
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I've been running more tests of BAOAB. In #2396 and #2520 I tested it on alanine dipeptide in a box of water, using hbond contraints and rigid water. I found that it produced excellent potential ene…