<br><br><div class="gmail_quote">On Sat, Jun 18, 2011 at 4:13 PM, <a href="mailto:chris.neale@utoronto.ca">chris.neale@utoronto.ca</a> <span dir="ltr"><<a href="mailto:chris.neale@utoronto.ca">chris.neale@utoronto.ca</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">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></blockquote><div>Probably. To make sure check the constraint-algorithm selected in your mdp. </div><div>BTW: If you want to use large timecheck you should normally use constraints=all-bonds and lincs-order=6.</div>
<div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<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></blockquote><div>This is also done with P-LINCS. Not sure whether one should sign something regarding the construction/usage of v-sites.</div><div><br></div><div>Roland</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<br>
Thank you,<br>
Chris.<br>
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</font></blockquote></div><br><br clear="all"><br>-- <br>ORNL/UT Center for Molecular Biophysics <a href="http://cmb.ornl.gov">cmb.ornl.gov</a><br>865-241-1537, ORNL PO BOX 2008 MS6309<br>