<div dir="ltr"><br><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Jan 27, 2015 at 11:26 AM, "Pablo García Risueño" <span dir="ltr"><<a href="mailto:Risueno@physik.hu-berlin.de" target="_blank">Risueno@physik.hu-berlin.de</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear Gromacs developers<br>
<br>
My name is Pablo G. Risueño, I am a postdoc researcher at the Humboldt<br>
University of Berlin. I am currently working with some colleagues in the<br>
development of new constrained MD schemes.<br>
<br>
A few years ago I had a conversation with prof. B. Hess, where he told me<br>
that both SHAKE and LINCS can make a MD simulation to crash (specially for<br>
large systems with many time steps). We would like to analyse the problem,<br>
so we would like to have some example(s) of simulation where such crash<br>
happens. We would need the Gromacs input file, and the<br>
coordinates/velocities files at the step before the crashing. May anybody<br>
help us?<br></blockquote><div><br></div><div>Hi,</div><div><br></div><div>This is one of the easier problems in molecular dynamics. :-) You can probably take anybody's MD tutorial, multiply the time step by 10 and observe the simulation blow up from numerical instability. The constraint algorithm is often the first thing to fail, but it is not itself the problem. It seems to me that 99+% of the time the user has not prepared the system or model physics well enough, and most of the rest of the cases are code bugs.</div><div><br></div><div>It is not clear to me that even if a constraint algorithm could be designed to satisfy such cases (of poor user input), that having it would be a good thing. It is irritating to have a simulation blow up because you were too rough with it, but it could well be worse to have your simulation succeed with only subtle evidence of the original problem.</div><div><br></div><div>Cheers,</div><div><br></div><div>Mark</div></div></div></div>