[gmx-users] rlist and rcoulomb
Mark.Abraham at anu.edu.au
Fri Oct 22 17:31:12 CEST 2010
On 23/10/2010 2:20 AM, Swarnendu Tripathi wrote:
> Thanks for the reply.
> So, can I think that when I set rcoulomb > rlist then the Coulomb (LR)
> energy term is providing some kind of correction over the Coulomb (SR)
> energy term.
Yes. It's implementing the idea mentioned in the first para of manual
> On Thu, Oct 21, 2010 at 4:39 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
> 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.
> Any suggestion is appreciated and thanks in advance.
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
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