[gmx-users] the growth of the molecule

Mon Sep 22 21:09:57 CEST 2014

On Mon, Sep 22, 2014 at 7:33 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 9/22/14 10:45 AM, Александр Селютин wrote:
>
>> 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?
>>
>>
> I don't know that there is a good solution.  What you've outlined also
> doesn't seem very reliable, because you're causing serious perturbations to
> the system every 2 ps, so the outcome of the previous simulation is
> basically lost because you have changed the coordinates and perturbed the
> solvent around the polymer. So you basically have a certain number of
> unequilibrated polymer systems of varying size.  It doesn't help you to
> determine much of anything.
>
> MD is great for simulating nonbonded aggregation/assembly, but it is not
> trivial to do something involving covalent bonds in classical MD.
>
>
>

If you want to study dynamic of growth of materials via formation of
chemical bonds
(covalent, ionic and even metallic), perhaps empirical reactive FFs might
be
acceptable choices in terms of cost and accuracy BUT those are not
implemented
in GROMACS as far as I know. You need try them using LAMMPS, ADF, ReaxFF
codes,.....

Rasoul

>
>  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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>>
>>
>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
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