<div dir="ltr"><div>Thanks for all the replies. </div><div><br></div>pdihs() appears to be the main functon that also calls dopdihs(). <div><br></div><div>Is it OK to intorduce the conditional into pdihs(), and bypass even calling dopdihs() if r_kj ( as reported by calling dih_angle() ) is less then threshold? </div>
<div><br></div><div>I will go for this as it makes sense to me, if it is not directly colliding with something that I don't know about. </div><div><br></div><div>I would truly appreciate if someone with intimate knowledge of the code comment on the acceptability of this approach. I am not entirely comfortable acting on such limited knowledge. </div>
<div><br></div><div>I am already familiar with the -noddcheck option, thanks to your mentioning it previously, Dr. Hess, but thank you very much. </div><div><br></div><div>Regards</div><div><br></div><div>Murat</div></div>
<div class="gmail_extra"><br><br><div class="gmail_quote">On Wed, Sep 25, 2013 at 3:53 PM, Berk Hess <span dir="ltr"><<a href="mailto:hess@kth.se" target="_blank">hess@kth.se</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="im">On 09/25/2013 02:31 PM, Erik Lindahl wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Type 1 is a "proper dihedral", which means "do_pdihs()" ;-)<br>
<br>
However, beware if you are running in parallel with domain decomposition - even if _you_ won't evaluate the interaction when it is beyond the cutoff, Gromacs will complain if it cannot communicate the coordinates for you.<br>
</blockquote></div>
You can turn off that check by running mdrun -noddcheck<br>
<br>
Cheers,<br>
<br>
Berk<div class="HOEnZb"><div class="h5"><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Cheers,<br>
<br>
Erik<br>
<br>
On Sep 25, 2013, at 2:25 PM, Mark Abraham <<a href="mailto:mark.j.abraham@gmail.com" target="_blank">mark.j.abraham@gmail.com</a>> wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I forget which, but you will anyway need a test case that shows you<br>
that your modification is working correctly. Make a small but relevant<br>
system and use it with mdrun -rerun to compute single-point energies<br>
and forces. Then hack functions one by one by forcing them to output<br>
zero until you see an effect with mdrun -rerun. Now you know what<br>
function to work on, and have your test machinery ready to use!<br>
<br>
Mark<br>
<br>
On Wed, Sep 25, 2013 at 2:15 PM, MURAT OZTURK <<a href="mailto:murozturk@ku.edu.tr" target="_blank">murozturk@ku.edu.tr</a>> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hey guys,<br>
I am trying to introduce a small hack that will turn off dihedrals if the<br>
middle bond is longer than a threshold.<br>
<br>
It should be as simple as<br>
<br>
midDist= iprod(r_jk,r_jk)<br>
midDist *= gmx_insqrt(midDist)<br>
<br>
if ( midDist > threshold) {don't even bother calculating anything for this<br>
dihedral}<br>
else {continue as usual}<br>
<br>
But there are so many functions in bondfree.c. I need to locate that is<br>
responsible for regular, periodical dihedrals (type 1). Which one is this?<br>
My suspects are..<br>
<br>
dopdihs, dopdihs_XXXX (noener etc.) , pdihs, pdihs_XXXX (noener etc.)<br>
<br>
Is there any documentation I can look at to figure our what these do? There<br>
are not many comments within the code.<br>
<br>
I appreciate the input. This is all for a fancy coarse grained system.<br>
<br>
Murat<br>
<br>
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