Hello,
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.
Thanks,
Chris.
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