[gmx-users] Re: rvdw parameters (and other mdp stuff)

[Graham Smith]

> Especially the short-range cutoff (0.8) *SHOULD* *NEVER* *BE*
> *CHANGED*.  For the long range it is not so critical, but you would
> rather use 0.8/PME in stead of increasing the 1.4 long range
> cut-off. 

Just to make sure I've got this clear, 
with ffG43*, 

rlist                    = 0.8
coulombtype              = PME
rcoulomb-switch          = 0
rcoulomb                 = 0.8 

vdwtype                  = Cut-off
rvdw-switch              = 0
rvdw                     = 1.4

(...and not rlist=rcoulomb=0.9, rvdw=1.4, which I started using a
couple of months ago when I switched to PME. I got this by
misunderstanding the manual (section 4.6.2) and mdp_opt.html; perhaps
a note could be added to say that it applies only to ffgmx? Or is
increasing rlist not as serious as decreasing it?) 

What parameters should I use with the new opls ff? Kaminski et al, J
Phys Chem B 201 105 6474, state what cutoffs they've used only for
their simulations of methanethiol and ethanethiol; 
unless I'm missing it, they don't mention the conditions for the 
simulations of peptides. They say 

intermolecular interactions were truncated at 11A, with the standard
correction for the interactions beyond that radius [ref to 1984 JACS
paper]. The ES interactions were quadratically feathered to zero over
the last 0.5A before the cutoff. 

So if they're the same that would mean for ffopls protein simulations 

rlist                    = 1.1
coulombtype              = PME
rcoulomb-switch          = 1.05
rcoulomb                 = 1.1

vdwtype                  = Cut-off
rvdw-switch              = 0
rvdw                     = 1.1

? 

Do I need to switch on DispCorr? 

While we're at it, I have always used a different temperature coupling
group for each type of [ molecule ] in the .top, so I have e.g.

tcoupl                   = nose-hoover
tc-grps                  = Protein  SOL NA+ CL-
tau-t                    = 5 5 5 5
ref-t                    = 300 300 300 300

This has propagated from an mdp I was given years ago (even though
I've switched tc algorithm). But I've never really seen why it
isn't always best just to tcoupl the whole system. I would think
averages should be the same, but T-fluctuations will be reduced by
somthing like sqrt(N_grp/N_system) with the groups coupled
separately. Any comments? 

Thanks for the help, 

Graham 

########################################################################

Dr. Graham R. Smith, 		       Department of Biological Sciences,  
Biomolecular Modelling Laboratory,     Biochemistry Building,              	
Cancer Research UK, 		       Imperial College of Science,        	
44 Lincoln's Inn Fields, 	        Technology & Medicine,             	
London WC2A 3PX,		       London SW7 2AZ,                     	
U.K. 				       U.K.                                	
Tel: +44-(0)20 7269 3348 	       Tel: +44-(0)20 7594 5737            	
email: graham.smith at cancer.org.uk	
URL: http://www.bmm.icnet.uk/~smithgr