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GROMACS version: 2024.2
GROMACS modification: No
Hello, I'm currently analyzing a few molecules to cross 1,2-Dioleoyl-sn-Glycero-3-Phosphocholine
(DOPC) bilayer. I tried creating DOPC bilayer us…
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Hello,
my name is Alexander Vogel and I'm trying to add a new simulation with 3 runs (7 microseconds each) to the databank (DOIs: 10.5281/zenodo.10635871 - 10.5281/zenodo.10635875 - 10.5281/zenodo.…
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I'm back for another problem related to #3152 :)
So this is a problem caused by a disagreement about how to label terminal caps. From the [CHARMM-GUI FAQ](https://charmm-gui.org/?doc=faq)
> Som…
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Hi,
I ran a lipid bilayer simulation for 500 ns and when I am trying to calculate order parameter for POPC for a trajectory beginning from the simulation it runs fine. But I want to consider the las…
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Hello,
I have noticed that eventhough you can select chains as :A, it seems not to be possible to select by segid (MDAnalysis) or segname (vmd) like PROA. This would be usefull since psfs don't see…
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FATAL ERROR: redistrib lone pair forces: no Lphost exists for LP 15891
My ligand have lone pairs. I set the "lonepairs on" in the .conf file and it run smooth however sometimes it give the above er…
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Would it be possible to share some snapshots of the MD carried out on protein M in the presence of a membrane?
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It has been suggested that providing molecular movies from the CHARMM trajectories might be a nice feature to add to BilboMD
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Hello,
I used Charmm-gui to insert a complex protein into a custom lipid membrane (POPE,POPG), and I ran the simulation in Gromacs (using the amber forcefields). Now, we need to move the system to th…
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Hi OpenMM community,
I'm trying to benchmark openMM 8.1.0 and 8.1.1 on Frontier (OLCF), given the reported improvements in the OpenCL implementation.
However, I'm getting this error:
```Traceba…