provided that your box is large enough (at least box is
52**3, to hold
the cylinder), the polymers are in fact quite dilute.
You could just set
them up as tilted straight lines starting from their
thus avoiding any overlap. Then you don' t need to
warmup and should
never encounter large energies.
On 19.03.14 16:31, Stefan Kesselheim wrote:
> Dear Roya,
> On Mar 19, 2014, at 4:24 PM, roya moghaddasi <address@hidden
>> Dear Stefen,
>> Thank you for your reply,
>> My potentials are FENE, Coulomb(after
warm_up), LJ 6-12 between particles, LJ 3-9 between
particles and constraint.
>> The error " constraint violated by particle
...." constantly occured in my system, so I had
emailed to the mailing list and some one in your group
said that I should at first use the reflecting
constraint and after warm_up delete and redefine the
constraint without reflection and in this way I solved
my problem. I don't think there is some thing wrong
>> You said I shouldn't cap the interaction
between particles and the cylinder (3-9 LJ), but how
can I do that? How can I sepperate this interaction
from others during warm_up? Can you please explain it
> Every LJ-interaction has its own capping
parameter (see documentation of inter lennard-jones).
I'm not sure if you need to switch on this capping, by
inter forcecap individual or if it just works. Please
have a look at the user's guide.
JP Dr. Axel Arnold
ICP, Universität Stuttgart
70569 Stuttgart, Germany
Tel: +49 711 685 67609