[gmx-users] the growth of the molecule

Mon Sep 22 20:33:33 CEST 2014

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.

-Justin

> 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
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