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On 23/10/2010 2:20 AM, Swarnendu Tripathi wrote:
<blockquote
cite="mid:AANLkTiksAih2aHo+a+zUAavO9zcdZKYw1UFS-r-bDgKL@mail.gmail.com"
type="cite">Hello,<br>
<br>
Thanks for the reply.<br>
<br>
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.<br>
</blockquote>
<br>
Yes. It's implementing the idea mentioned in the first para of
manual section 3.4.7<br>
<br>
Mark<br>
<blockquote
cite="mid:AANLkTiksAih2aHo+a+zUAavO9zcdZKYw1UFS-r-bDgKL@mail.gmail.com"
type="cite"><br>
-Swarnendu<br>
<br>
<div class="gmail_quote">On Thu, Oct 21, 2010 at 4:39 PM, Justin
A. Lemkul <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid
rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left:
1ex;">
<div class="im"><br>
<br>
Swarnendu Tripathi wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px
solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex;
padding-left: 1ex;">
Dear gromacs users,<br>
<br>
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.''<br>
<br>
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. <br>
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 <br>
</blockquote>
<br>
</div>
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.
<div class="im">
<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px
solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex;
padding-left: 1ex;">
how the Coulomb (LR) is calculated? Is it calculated in
the same way as Coulomb (SR) and simply denoted as
Coulomb (LR), since rlist < <br>
</blockquote>
<br>
</div>
Probably in the same was as Coulomb (SR), but with the
frequency described in the manual.
<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px
solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex;
padding-left: 1ex;">
rcoulomb? Or, in this case it is suggested that I should
always use rlist=rcoulomb.<br>
<br>
</blockquote>
<br>
</div>
Using rlist=rcoulomb is fairly common for many force fields,
but whether or not this is required for your model is up to
you.<br>
<br>
-Justin
<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px
solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex;
padding-left: 1ex;">
Any suggestion is appreciated and thanks in advance.<br>
<br>
-Swarnendu<br>
<br>
</blockquote>
<br>
</div>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a moz-do-not-send="true" href="http://vt.edu"
target="_blank">vt.edu</a> | (540) 231-9080<br>
<a moz-do-not-send="true"
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
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