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Mark Abraham skrev 2011-03-24 06.52:
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On 24/03/2011 4:38 PM, Swarnendu Tripathi wrote:
<blockquote
cite="mid:AANLkTi=zOWw0GDuj50EF4hkqRX=zjKK5677ejKdBhdzu@mail.gmail.com"
type="cite">Hi all,<br>
<br>
Thank you for the reply. The answer I got for the second
question about table-extension, I understand and agree with
that. <br>
<br>
Regarding my first question I asked, I did not get any error
with grompp even when I tried rlist=rvdw=2.0 and rcoulomb=0. For
this I used the no cut-off conditions which I have mentioned
below in my previous e-mail. I am using Gromacs-4.0.7. Any
further suggestions or comments will be very helpful.<br>
</blockquote>
<br>
VDW interactions normally become insignificant much faster than
Coulomb interactions, so treating all Coulomb interactions and
only some VDW interactions is logical. However, performing the
search for neighbours takes time, and given that you are computing
the distances already for their Coulomb interaction, it is
probably cheaper just to compute all the VDW interactions, i.e.
rlist=rvdw=0. This might be different if you had a lot of atoms
that had zero partial charge.<br>
<br>
Mark<br>
</blockquote>
In addition, depending on your system, the collective long-range
attraction from VdW interactions may not be insignificant. And since
you're simulating in vacuo, I guess you have an inhomogeneous
system, and dispersion corrdection may not be adequate. That's
further reason to have infinite VdW cut-offs too. And, as mark
mentioned, the distances are calculated anyway, so computing VdW
will not add that much to your simulation time.<br>
<br>
Erik<br>
<blockquote cite="mid:4D8ADC06.8030101@anu.edu.au" type="cite"> <br>
<blockquote
cite="mid:AANLkTi=zOWw0GDuj50EF4hkqRX=zjKK5677ejKdBhdzu@mail.gmail.com"
type="cite">
<div class="gmail_quote">On Thu, Mar 24, 2011 at 12:17 AM, Mark
Abraham <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
<div class="im">On 24/03/2011 1:34 PM, Itamar Kass wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;"> Hi Swarnendu,<br>
<br>
grompp will return errer unless rlist=rcoulomb=rvdw=0,
so you should stick to it.<br>
<br>
Cheers,<br>
Itamar<br>
<br>
On 24/03/11 1:13 PM, Swarnendu Tripathi wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt
0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;"> Hello everybody,<br>
<br>
I want to use the no cut-off option in gromacs for the
electrostatic interactions. In manual it says for this
I need to define: pbc=no; nstlist=0; ns-type=simple
and rlist=rcoulomb=rvdw=0 in the .mdp file.<br>
<br>
My questions are:<br>
<br>
1. If I choose rcoulomb=0 and rlist=rvdw=2.0 is that a
problem? Do you always recommend to use
rlist=rcoulomb=rvdw=0 for no cut-off option?<br>
<br>
2. How should I choose the table-extension parameter
now? Before, with pbc=xyz (with cut-off) I used
table-extension=rvdw+1/2*length of the longest
diagonal of the box (approximately). I am also using a
tabulated potential.<br>
</blockquote>
</blockquote>
<br>
</div>
Since there is effectively no box once pbc=no, your tables
need only be as long as the longest possible interaction,
plus some margin for when the structure rearranges.<br>
<font color="#888888"> <br>
Mark</font>
<div>
<div class="h5"><br>
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<pre class="moz-signature" cols="72">--
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
<a class="moz-txt-link-abbreviated" href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a> <a class="moz-txt-link-freetext" href="http://folding.bmc.uu.se/">http://folding.bmc.uu.se/</a>
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