[gmx-users] rlist and rcoulomb

[Justin A. Lemkul]

Swarnendu Tripathi wrote:
> Dear gromacs users,
> 
> In section 4.6.3 of gromacs 4 manual it says ``... the interactions 
> between pairs that do not fall within rlist but do fall within 
> max(rcoulomb,rvdw) are computed during neighbor search (NS), and the 
> forces and energy are stored separately, and added to short-range forces 
> at every time step between successive NS.''
> 
> Now I find that if I use rlist (= rvdw) = rcoulomb then I only have 
> Coulomb (SR) values in the md.log file but if I use rlist (= rvdw) < 
> rcoulomb then I get both Coulomb (SR) and Coulomb (LR) values in the 
> md.log. In both cases I have assigned vdwtype=user and also 
> rcoulomb=user for a tabulated potential that I use. 
> 
> Now, my question is how in the second case when rlist < rcoulomb I am 
> getting the Coulomb (LR) values in md.log? Particularly, I want to know 

You have twin-range interactions.  Some interactions do not occur within rlist, 
but occur within rcoulomb, which is beyond rlist.  This is exactly the case 
stated in the manual.  If rlist = rvdw, then max(rvdw,rcoulomb) finds that 
rcoulomb is larger than rvdw and thus defines the outer bound of the twin-range 
setup.

> how the Coulomb (LR) is calculated? Is it calculated in the same way as 
> Coulomb (SR) and simply denoted as  Coulomb (LR), since rlist < 

Probably in the same was as Coulomb (SR), but with the frequency described in 
the manual.

> rcoulomb? Or, in this case it is suggested that I should always use 
> rlist=rcoulomb.
> 

Using rlist=rcoulomb is fairly common for many force fields, but whether or not 
this is required for your model is up to you.

-Justin

> Any suggestion is appreciated and thanks in advance.
> 
> -Swarnendu
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================