[gmx-users] pdb2gmx -ff oplsaa -water tip4p / cut-offs for oplsa

Abil Aliev abil4616 at yahoo.co.uk
Tue Dec 14 14:53:54 CET 2004

with the above i get OW1,HW1,HW2 and HW4 for crystallogrphic waters 
which are labelled as HO4. after editconf/genbox -cs tip4p i get a 
different type for added water with HW1 above replaced by MW1. i can 
change HW1 to MW1 and HO4 to HOH before genbox to get the grompp 
working, but is this the right way to proceed?

Also, are there any typical cutoffs dictated by the choice of oplsa for 
proteins. I came across the following in the archives (~2002)

rlist = 1.1
rcoulomb= 1.1 (PME)
rvdw = 1.1 (Cut-off)
rvdw-switch = 0

but the original JACS paper (1996,118,11228) talks about cutoffs of 15A 
for amides!? so if we are using PME, would rlist=rcoulomb=0.9 (no 
switching), rvdw=1.4 (cut-off) and nslist=5 be resonable with oplsa?

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