Pages

▼
Showing posts with label gromacs. Show all posts
Showing posts with label gromacs. Show all posts
23 October 2013

524. Generating bonds, angles and dihedrals for a molecule for GROMACS

›
Generating bond, angle and dihedral parameters for GROMACS molecular dynamics simulations is a real PITA when it comes to reasonably large a...
26 April 2013

396. Compiling gromacs 4.6 with gpu support, openblas and fftw3 on debian wheezy

›
NOTE: with ACML my performance on my FX8150 and FX8350 nodes is only 25% of that with Openblas (double precision). Yes, for some reason gro...
3 comments:
20 September 2012

243. My own personal benchmarks for NWChem, gromacs with atlas, openblas, acml on AMD and intel

›
Update: you can compile against acml on intel as well, and against mkl on amd. Still need to do some performance testing to see how well it ...
6 comments:
10 September 2012

230. ROCKS 5.4.3, ATLAS and Gromacs on Xeon X3480

›
After doing another round of ' benchmarks ' (there are so many factors that differ between the systems that it's difficult to te...
1 comment:
07 September 2012

229. Compile ATLAS (+ gromacs, nwchem) on AMD FX 8150 on Debian Testing (Wheezy)

›
Xianyi's openblas doesn't seem to be ready for AMD FX 8150 yet. I've played with ATLAS in the past, but  for some reason didn...
04 September 2012

227. New compute node using AMD FX-8150. Gromacs, nwchem performance/benchmarks

›
Update:  reconfiguring your nwchem binary using getmem.nwchem can speed things up considerably. Most of the runtimes are obtained without u...
17 May 2012

155. Gromacs with external fftw3 and blas on debian testing

›
This is based on  http://verahill.blogspot.com.au/2012/03/building-gromacs-with-fftw3-and-openmpi.html Make sure your build environment is...
10 May 2012

147. Oniom in nwchem -- with a little bit of help from gromacs and openbabel

›
Example -- I want to do explicit solvent modelling of methanol in water. This is obviously an articifical approach, but generally applicable...
24 January 2012

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 sh...
18 January 2012

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 ...
5 comments: