[gmx-users] the growth of the molecule

[Tamas Karpati]

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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