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Hello,
So i have trying to perform a 2D meta-eABF using path collective variable as reaction coordinate. To generate the PMF i use abf_integrate, however the PMF generated looks non ideal. Furthermor…
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I am a little curious about the harmonic walls implementation with extended Lagrangian dynamics. Is applying the wall potential to actual CVs theoretically better than to extended CVs?
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Hi Wei,
I'm having troubles reproducing your results for alanine dipeptide using this MESA program. I am running the exact same parameters as stated in your paper Molecular Enhanced Sampling with Aut…
ghost updated
5 years ago
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I have a simple question what is the difference between the above mentioned methods
For me VAC metadynamics is very similar to TICA metadynamics with some optimized scheme to give co-efficients to …
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Dear Colvars developers,
Using "cv save", I can only get the metadynamics output file, but not ABF files. I guess this is because "cv save" calls write_output_files(), which is rewritten by colvarb…
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Is there any chance of getting these PDBs as mentioned in the plumed file so that one try to reproduce the exact work with similar settings?
RMSD REFERENCE=../pdbs/0.pdb TYPE=OPTIMAL LABEL=RMSD_0
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If fittingGroup could be used without refPositionsFile to reference another group of atoms in the simulation, this would allow, for example, constraining the relative tilt of two groups.
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Dear Developer,
I used tica_metadynamics.plumed_writer to render tiC in a Plumed like file. I am using distance between CA of 35--79 and 215--293 during featurization extract. My only doubt is `mea…
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Hello,
I succesfully installed tica_metadynamics after installing plumed and all the dependencies indicated in requirements.txt.
However, when I try to execute the test_project_setup.py I got the fo…
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The UFED (Unified Free Energy Dynamics) is implemented in the PLUMED 2 already? Since I cannot find it, I found only that the method is implemented in the PLUMED 1.3 release and was successfully used …