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@hiddenTel: +49 711 685 67609