[gmx-users] the growth of the molecule

[Александр Селютин]

Thanks to everyone
I have idea that I can stop simulation, change topology(move end of
molecule, add new atoms) and start again. It should be repeated every 2 ps.
But it can be very slowly. Does anybody know how to do it more correctly?

2014-09-18 20:03 GMT+07:00 Tamas Karpati <tkarpati at gmail.com>:

> Dear Alexander,
>
> As Vitaly has already suggested, it is possible to simulate growth.
> I'd, on the other hand, underline what Micholas has said.
> It may take some planning. Here are a few ideas how to do it.
>
> 1. If you are simulating cleaving/forming bonds, the topology would change
> which is difficult for normal MD runs. If, however, running just few steps
> (or probably a single step) MD job and analysing/regenerating the topology
> after each such step (by your specific scripts) you may be fine.
> It can take some coding.
>
> 2. You can still go on by replacing explicite bonds by Morse
> or LJ potentials (or using any tabled ones). Although such model can
> be poor in describing the underlying chemistry a good fitting of
> Morse/LJ/etc.
> can give you an acceptable rate for the polymerisation. This way bonds
> could be described by formally non-bonding interactions and the whole
> system is modelled as an interacting set of individual single atom ions.
> A complete replacement of all the bonds by non-bonding interaction
> potentials will give you a bond-less and angle-less etc. TOP file.
> It can be done in parts, too, in which case just some kinds of bonds
> (those that cleave or form) would be replaced. It may take lots of
> preparation but I think its viable.
>
> 3. Sorry, I know nothing about special force fields created for sims of
> reactions. Probably those would be your tools.
>
> HTH,
>   toma
>
>
> On Thu, Sep 18, 2014 at 2:10 PM, Smith, Micholas D. <smithmd at ornl.gov>
> wrote:
> > I should clarify, If you are not concerned with the formation of
> covalent bonds, you can simulate growth, to some extent. Protein
> aggregation, for instance, can be studied with MD because of this; so if
> you are only interested in the early assembly, and not with electronic
> structure/covalent bonding, than you are ok. I had interpreted your
> question to be related to bonding, not just early assembly/aggregation.
> >
> > As far as adding units at a given time, I don't think gromacs can do
> that, as it would require your topology to change while the simulation was
> running (i.e. adding more molecules to your system while it is running).
> Now you could run multiple simulations of the polyethylene chain at
> different lengths with a single unit free in solution, and watch how the
> chain increases, but I don't think you could run a single simulation where
> you added monomer units on the fly.
> >
> > -Micholas
> > ________________________________________
> > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Dr.
> Vitaly Chaban <vvchaban at gmail.com>
> > Sent: Thursday, September 18, 2014 2:43 AM
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] the growth of the molecule
> >
> > Why not? Your interaction potential is responsible for everything.
> >
> >
> >
> > Dr. Vitaly V. Chaban
> >
> > Виталий Витальевич ЧАБАН
> >
> >
> > On Mon, Sep 15, 2014 at 7:27 PM, Александр Селютин <saga111a at gmail.com>
> wrote:
> >> Can the gromacs simulate the growth of the molecule?
> >> For example, does it allow to add units to the polymer chain at certain
> >> times?
> >> More specifically, it is the increase the chain length of the
> polyethylene.
> >>
> >> Thanks!
> >> --
> >> Regards,
> >> Alexander Selyutin
> >> --
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-- 
Regards,
Alexander Selyutin