User Tools

Site Tools


exercises:2015_cecam_tutorial:forcefields

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision
Previous revision
exercises:2015_cecam_tutorial:forcefields [2015/09/01 21:42]
mwatkins
exercises:2015_cecam_tutorial:forcefields [2015/09/02 05:07]
mwatkins
Line 15: Line 15:
   {{http://​www.cp2k.org/​_media/​exercises:​2015_cecam_tutorial:​vmd_solvate.png}}   {{http://​www.cp2k.org/​_media/​exercises:​2015_cecam_tutorial:​vmd_solvate.png}}
   ​   ​
-Now you should have solvate.psf and solvate.pdb in your directory, which contain the coordinates and connectivity information of the solvated protein. For some proteins you might now need to add ions into the solvent to neutralize the system, but we're OK with ubiquitin.+Now you should have solvate.psf and solvate.pdb in your directory, which contain the coordinates and connectivity information of the solvated protein. Open the .psf file edit the first line to simple read PSF. For some proteins you might now need to add ions into the solvent to neutralize the system, but we're OK with ubiquitin.
  
 At this point we're nearly ready to run CP2K. First we need to get hold of the forcefield files. The CHARMM forcefields are distributed from the MacKrell group website {{http://​mackerell.umaryland.edu/​charmm_ff.shtml}}. Download toppar_c31b1.tar.gz,​ extract it with something like tar -zxvf toppar_c31b1.tar.gz. ​ At this point we're nearly ready to run CP2K. First we need to get hold of the forcefield files. The CHARMM forcefields are distributed from the MacKrell group website {{http://​mackerell.umaryland.edu/​charmm_ff.shtml}}. Download toppar_c31b1.tar.gz,​ extract it with something like tar -zxvf toppar_c31b1.tar.gz. ​
Line 138: Line 138:
  
 We take the coordinates from previous minimization run using the external restart option in CP2K. Hopefully this works for you and you can explore the MD facilities in the code. You'd need to equilibriate for quite some ns before starting production, maybe including some NPT to make sure the box size is correct. We take the coordinates from previous minimization run using the external restart option in CP2K. Hopefully this works for you and you can explore the MD facilities in the code. You'd need to equilibriate for quite some ns before starting production, maybe including some NPT to make sure the box size is correct.
 +
 +(This exercise is heavily based on material I-Feng William Kuo (Lawrence Livermore National Laboratory) presented at previous CP2K workshops)
 +
  
    
exercises/2015_cecam_tutorial/forcefields.txt ยท Last modified: 2015/09/02 05:07 by mwatkins