[gmx-users] 4fs timestep in gromacs 4.0

chris.neale at utoronto.ca chris.neale at utoronto.ca
Thu Oct 30 03:32:25 CET 2008


I am interested in trying the 4 fs timestep options for an  
opls-protein/tip4p-water system. I will of course do some quick NVE  
tests to ensure that the energy does not drift massively, and also do  
some other tests that look at some properties that should equilibrate  
rather quickly. Also, I realize that there is no substitute for  
reading the literature.

Still, I am hoping to get some indication of how this was intended to  
be utilized in gmx4. Can I just run pdb2gmx -vsite -heavyh and apply  
LINCS to all-bonds? The information in the gmx4 manual is nicely  
detailed about how each type of hydrogen should be treated, but I am  
not clear how to achieve this in my .top.

Searches for vsite and heavyh reading only the 2008 posts did not give  
me much indication about this.


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