On Sat, Nov 17, 2018 at 7:38 PM Lee <liuchongm...@gmail.com> wrote:
>
> The lammps dump files are attached. What's the meaning of layering as you
> said?
I was referring to the RDFs, which have some big zickzack pattern in there.
Christoph
>
> 在 2018年11月17日星期六 UTC+8下午9:15:00，Christoph Junghans写道：
>>
>> On Fri, Nov 16, 2018 at 6:30 PM Lee <liucho...@gmail.com> wrote:
>> >
>> > Thanks for your reply. The attached files are the new rdf of the last
>> > iteration step with target rdf distributions. Is the trend correct? Does
>> > it converge if the iteration isn't interrupted? And do you have any
>> > suggestions of my setting file? Such as the postupdate options, or postadd
>> > options which can help it converges quickly.
>>
>> Looking at the pictures, it seems some layering is going on. So I
>> would have a look of the MD movie to see if something strange going
>> on.
>> Otherwise scaling the update might me a good idea, plus only updating
>> one interaction per iteration step.
>>
>> Christoph
>>
>> > Thanks again
>> >
>> > 在 2018年11月17日星期六 UTC+8上午12:58:44，Christoph Junghans写道：
>> >>
>> >> On Fri, Nov 16, 2018 at 6:23 AM Lee <liucho...@gmail.com> wrote:
>> >> >
>> >> > Hello votca users
>> >> > I‘m trying to get the cg potential of DGEBA using IBI method. One dgeba
>> >> > molecular is coarse grained with 3 beads, named as C A C. So in this
>> >> > system, there are two types of beads (C and A), one type of bond (C-A),
>> >> > one type of angle (CAC) and three types of non bonded interaction (CC,
>> >> > AA, CA). These target distributions and CG model are all obtained from
>> >> > lammps dump file manually. All of these target distributons have been
>> >> > smoothed.
>> >> > Firstly, I do the ibi for all objects in order to get the bonded
>> >> > potential table from step_001. Then, I just do the ibi process for non
>> >> > bonded interaction. But with the process of iteration going on, the
>> >> > error "Pair distance < table inner cutoff" occured during the MD
>> >> > simulation by LAMMPS. And the rdf seems not to converge. I have tried
>> >> > several times with different parameter for <table_begin>, but the error
>> >> > still occurs at some iteration step. The configuration dump from lammps
>> >> > shows that some beads get together, which is unnormal.
>> >> > The attached files are the setting files and target distributions. Can
>> >> > somebody point out my mistake? How could I modify my setting file?
>> >> > I would really appreciate your advise. Thanks in advance!
>> >> It seems you are doing things pretty correct already, sometimes it
>> >> helps to add an additional purely repulsive interaction in LAMMPS to
>> >> prevent close contacts ("Pair distance < table inner cutoff").
>> >>
>> >> Christoph
>> >> > Lee
>> >> >
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>> >>
>> >>
>> >> --
>> >> Christoph Junghans
>> >> Web: http://www.compphys.de
>> >
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>>
>>
>> --
>> Christoph Junghans
>> Web: http://www.compphys.de
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