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--- exercises:2015_cecam_tutorial:forcefields [2015/09/01 21:39] – 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}}
-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.
@@ Line 69: / Line 69: @@
 </code>
-Now we can start to equilibriate the system in MD
+Now we can start to equilibriate the system in MD. Make a new input file as follows, and run it in the same directory (or tell it where the restart file from the minimization is)
 <code>
@@ Line 137: / Line 137: @@
 </code>
-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.
+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)