How about NAMD 2.9 and FirePro for molecular dynamics calculations?

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I would like to perform MD simulation study for CYP450 proteins in gromacs 4.6.7 with gromos53a6.ff. When I prepare the system for simulation, i have got error that gb_, ga_ and gd_ were not found...

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How can one transfer all ligands from templates to final homology model?

I have 3 X-ray structures with co-crystallized ligand in active site. How should I actively copy all ligand in this same position from all temple to the final homology models? I perform homology...

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Can anyone help with molecular dynamics and protein equilibration?

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Which of the CHARMM force field versions is better for protein structural biology studies?

Charmm27 or Charmm36?

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What kind of analyses should I use to determine the affinity of peptide-protein interaction after molecular dynamics?

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Is there a good way to prepare molecular dynamics simulations?

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Hiqmet Kamberaj

You may find the answer of your question following this link:

http://www.ks.uiuc.edu/Research/namd/2.9/features.html

Tomasz Molcan

Yes I know that NAMD can use CUDA cores for calculations, but I like to know is there possible to use Radeon GPU for example FirePro by NAMD? Can anyone use AMD cards for NAMD calculations?

Denish Poudyal

Not yet...AMD has no ability for CUDA.