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