Generating bond, angle and dihedral parameters for GROMACS molecular dynamics simulations is a real PITA when it comes to reasonably large a...
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Showing posts with label gromacs. Show all posts
Showing posts with label gromacs. Show all posts
56. Gromacs -- setting up and running energy minimisation of methanol in water. Using itp files
* First browse through this tutorial. * I'm not an expert at GROMACS -- I'm writing this up as I am learning myself. Use what I sho...
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53. GROMACS -- carbon dioxide in water. Example
I'm new to GROMACS, so don't follow what I've done blindly. To get started you need a .top and a .gro file. The .gro file is no...
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49. Gromacs -- hangs on multicore when doing normal mode analysis
Symptom: when doing mdrun -s nm.tpr -mtx nm.mtx -v -deffnm nm on a system with 637 atoms you end up with: ...Finish step 636 out of 637 and ...
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46. A VERY rough approach to "benchmarking" gromacs (unscientific) on debian
Here's a comparison between different hardware and binaries which were built as described in http://verahill.blogspot.com/2012/01/debia...
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