Thanks Axel. Basically I learned MD and lammps all by myself, since I changed my research direction and there are not many surrounding people that can offer help. Will inform you if there is any progres, or lammps problems.
> 发件人: "Axel Kohlmeyer" <akohlmey@...24...>
> 发送时间: 2018-04-24 23:51:29 (星期二)
> 收件人: "徐浩" <xuhao@...6726...>
> 抄送: "LAMMPS Users Mailing List" <firstname.lastname@example.org>
> 主题: Re: [lammps-users] Bad dynamics
> please note, that what you are asking about is how to set up,
> validate, and interpret MD simulations and the corresponding force
> fields. none of that is directly linked to LAMMPS, but applies to all
> MD codes.
> as i already suggested in a previous response, you need to discuss
> with your adviser or have you adviser identify a competent
> collaborator to help, train, and advise you on these topics.
> On Tue, Apr 24, 2018 at 10:51 AM, 徐浩 <xuhao@...6726...> wrote:
> > Dear All，
> > I recently simulated crosslinked epoxy resins. I encountered problem of
> > missing bonded atoms for quite a while. When using LJ potential (dreiding
> > forcefield), everything is fine, but when switching to X6 potential (for
> > relaxation after the crosslinking process using LJ potential), the run crash
> > all the time at a certain step, although I have adjusted the
> > timesteps,neighbouring list and so on.
> > I asked a researcher who has done relevant simulation. He told me that he
> > also has missing atoms when there is atom type of H__A (in dreiding, H__A is
> > Hydrogen possible of forming h bond). And then he changed H__A to H_(normal
> > hydrogen), the problem was solved. The difference between H__A and H_ is
> > that the vdw interaction with a H__A is several orders lower than with H_. I
> > followed this way and no missing atoms were found anymore, and the
> > simulation can keep going. One question is that is it a really correct way
> > to change H__A to be H_ ? Will the results be not realistic ? Then I tried
> > to use another way to constrain H__A by fix shake and rattle, using
> please note, that if i answer any of these questions with "yes" or
> "no", there is not much of a value in it. it is *your* work, and *you*
> have to make this decision. you cannot put in your paper a statement
> like "i used this model parameters because some dude on a mailing list
> told me it was ok". you have to do the validation on your own, since
> you are responsible for your work and its correctness.
> > fix 101 all shake/rattle 0.0001 20 0 t 7 # the type of H__A is 7 in my data
> > file
> > but I still encounter missing atoms using either shake or rattle. Could
> > anyone help to see if I have provided an effective constraint?
> again, you are asking for the kind of help, that is the job of an
> adviser. a mailing list is a poor replacement for that.
> > Another question is more general. I understand that X6 potential provide
> > much softer cores compared with LJ. But why soft cores can cause bad
> > dynamics? And since these two potentials are quite different, leading to
> > much different densities for example, how can we judge which one is more
> > realistic and which one is not ?
> a potential is realistic if it reproduces properties of the simulated
> compound as good as it can be expected for the kind of model chosen
> and for as good as is needed for what you want to learn from a
> simulation. there is not simple: this is good, this is bad parameter.
> it always boils down to some kind of "it depends".
> > Regards
> > Hao
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> Dr. Axel Kohlmeyer akohlmey@...24... http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.