I want to check the changes in MD simulation for my protein in presence of Urea and GdnHcl. Can anybody suggest how can i do this?
See the tutorial of NAMD
http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/
http://www.ks.uiuc.edu/Training/Tutorials/
and user's guide
http://www.ks.uiuc.edu/Research/namd/2.12/ug/
Hi, you can search in NAMD tutorials (psf, pdb, ...)
Dear Vineeta,
we add ions with VMD plugin called autoionize . you can manipulate its script. you can consider GuHCl just like NaCl but urea like a single ion and replace it with NA for instance.
Bests
Farzane
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