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

David van der Spoel spoel at xray.bmc.uu.se
Tue Dec 14 15:46:24 CET 2004

On Tue, 2004-12-14 at 13:53 +0000, Abil Aliev wrote:
> 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)
> rcoulomb-switch=1.05
> 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?
Yes, I use that routinely.

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