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On 19/06/2011 6:56 AM, Roland Schulz wrote:
<blockquote
cite="mid:BANLkTimrgW8iXvPpZBtz6GwtQP0p-p4vEA@mail.gmail.com"
type="cite">My understanding is that the v-site algorithm is used
for the virtual sites and LINCS is used for bonds not involving
v-sites (and also angles if you choose contraint=angles). <br>
</blockquote>
<br>
Yep.<br>
<br>
Also, with the LINCS warning about over-rotation, I get that
regularly with initial equilibration under conditions such as yours.
It seems that somehow -XH3 groups do this (so far I've only seen it
in terminal NH3 and CH3). You can fix it by using a smaller time
step for a period, which gives the energy a better chance to
equipartition properly.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:BANLkTimrgW8iXvPpZBtz6GwtQP0p-p4vEA@mail.gmail.com"
type="cite">
<div class="gmail_quote">On Sat, Jun 18, 2011 at 4:40 PM, <a
moz-do-not-send="true" href="mailto:chris.neale@utoronto.ca">chris.neale@utoronto.ca</a>
<span dir="ltr"><<a moz-do-not-send="true"
href="mailto:chris.neale@utoronto.ca">chris.neale@utoronto.ca</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;">Thank you Roland.<br>
<br>
I did use:<br>
<br>
constraints = all-bonds<br>
lincs-iter = 1<br>
lincs-order = 6<br>
constraint_algorithm = lincs<br>
<br>
From looking at the manual, I figured that angle and bond
constraints<br>
would all be done by LINCS if I had done (A):<br>
<br>
pdb2gmx -vsite none<br>
constraints = h-angles<br>
(a combination that I have never tried)<br>
<br>
But when I use (B):<br>
<br>
pdb2gmx -vsite hydrogen<br>
constraints = all-bonds<br>
<br>
It seems possible to me that LINCS is not used but instead the<br>
position of the atom is simply built from a mathematical
function.<br>
Perhaps this all stems from my lack of thorough understanding
of<br>
LINCS, but it seems to me that there need be no iteration to
simply<br>
place an atoms based on virtual_sites3 (which are constructed
by<br>
pdb2gms -hydrogen)<br>
<br>
For now, I'll simply add a line to state that I built virtual
sites<br>
for hydrogen atoms to make it clear, but I'd still like to
understand<br>
the difference between options A and B, above, if you have
some time.<br>
<br>
Thank you again,<br>
Chris.<br>
<br>
<br>
<br>
<br>
<br>
On Sat, Jun 18, 2011 at 4:13 PM, chris.neale at <a
moz-do-not-send="true" href="http://utoronto.ca"
target="_blank">utoronto.ca</a> <<br>
chris.neale at <a moz-do-not-send="true"
href="http://utoronto.ca" target="_blank">utoronto.ca</a>>
wrote:<br>
<br>
> Dear Users:<br>
><br>
> If I create the topology of a peptide like this:<br>
><br>
> pdb2gmx -f protein.gro -vsite hydrogens<br>
><br>
> And then simulate it in vacuum, is lincs used at all? I
believe that<br>
> it is, as if I use a timestep that is too large then I
get LINCS<br>
> warnings about angles rotating more than 30 degrees, but
that warning<br>
> message could possibly have been written with the
assumption that I<br>
> used LINCS and not virtual hydrogens.<br>
><br>
Probably. To make sure check the constraint-algorithm selected
in your mdp.<br>
BTW: If you want to use large timecheck you should normally
use<br>
constraints=all-bonds and lincs-order=6.<br>
<br>
<br>
><br>
> Finally, is there a method that needs to be named or
cited in relation<br>
> to the fact that the angles are now constrained? Is that
also done<br>
> with P-LINCS?<br>
><br>
This is also done with P-LINCS. Not sure whether one should
sign something<br>
regarding the construction/usage of v-sites.<br>
<br>
Roland<br>
<br>
<br>
><br>
> Thank you,<br>
> Chris.<br>
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