On 5/14/13 10:27 AM, Joe Smerdon wrote:
Hi all,
First of all I'm new to md simulations, so if I am missing anything simple, I
would be grateful for any pointers, however small. I am trying to simulate
many small molecules on a substrate. I am restraining my substrate from moving
but allowing the molecules to do whatever they like. My steps are to minimise
my system (136 molecules on a 200Ax200A surface of about 4 layers, with 100A
vacuum), then to run an NVT simulation without pbcs (though I could use pbcs, I
just don't really need to for this). I am getting LINCS errors late on in the
simulations - they don't always cause a crash, but sometimes they do. I guess
it can't be insufficient minimisation if the errors arise after the simulation
has been underway for awhile (eg, step 15000, 8ps into a 50ps simulation), but
I don't really know what it can be. My timestep is 0.5 fs. I am just
experimenting at the moment, I intend to simulate for much longer when I get it
working.
I guess my question is: are LINCS errors that occur late in a simulation due to
poor minimisation, or not? If not, what other factors should I look at?
Failures at 8 ps are not considered late. There are a whole host of problems
that could be present, ranging from .mdp settings to topologies. See standard
advice for diagnosing at
http://www.gromacs.org/Documentation/Terminology/Blowing_Up.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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