[gmx-users] rlist and rcoulomb

[Mark Abraham]

On 23/10/2010 2:20 AM, Swarnendu Tripathi wrote:
> Hello,
>
> 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 
section 3.4.7

Mark
>
> -Swarnendu
>
> 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.
>
>     -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 <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>     ========================================
>     -- 
>     gmx-users mailing list gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>     http://lists.gromacs.org/mailman/listinfo/gmx-users
>     Please search the archive at
>     http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>     Please don't post (un)subscribe requests to the list. Use the www
>     interface or send it to gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101023/ef209152/attachment.html>