Hi,
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
mounting points,
thus avoiding any overlap. Then you don' t need to
warmup and should
never encounter large energies.
Axel
On 19.03.14 16:31, Stefan Kesselheim wrote:
> Dear Roya,
>
> On Mar 19, 2014, at 4:24 PM, roya moghaddasi <
address@hidden>
wrote:
>
>> 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
with it.
>> 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
more?
> 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.
> Cheers
> Stefan
--
JP Dr. Axel Arnold
ICP, Universität Stuttgart
Allmandring 3
70569 Stuttgart, Germany
Email:
address@hidden
Tel: +49 711 685 67609