Thank you very much. Really very helpful comments.<br><br>-Swarnendu<br><br><div class="gmail_quote">On Thu, Mar 24, 2011 at 1:52 AM, Mark Abraham <span dir="ltr"><<a 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 text="#000000" bgcolor="#ffffff"><div class="im">
On 24/03/2011 4:38 PM, Swarnendu Tripathi wrote:
<blockquote 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></div>
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><font color="#888888">
<br>
Mark</font><div class="im"><br>
<br>
<blockquote type="cite">
<div class="gmail_quote">On Thu, Mar 24, 2011 at 12:17 AM, Mark
Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">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>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><br>
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