[gmx-users] Turn on/off residues in gromacs

[Justin Lemkul]

On 10/23/18 8:08 AM, Quyen Vu Van wrote:
> Dear Justin,
> Thanks for your respond.
> What if I mean turn off residues just by remove the non-bonded term and
> then gradually adding non-bonded interactions back?

I understand exactly what you're trying to do and my comments are a 
direct response to that. This is not a reasonable model for what you 
want to study, for the reasons stated below.

-Justin

> Best regards,
> Quyen
>
> On Mon, Oct 22, 2018, 14:11 Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> On 10/22/18 7:29 AM, Quyen Vu Van wrote:
>>> Dear all,
>>> sorry for my unclear question,
>>> I attached here the quick draw picture of what I am saying, please take a
>>> look: https://www.dropbox.com/s/eycsm3qsywhgxjv/model.pdf?dl=0
>> What you are trying to do is both technically challenging and physically
>> questionable. The free energy options allow you to modulate the
>> interactions of a [moleculetype] with the remainder of the system; you
>> can't easily decompose individual residues of a protein, which is part
>> of a single [moleculetype]. You could manually define A- and B- states
>> in the topology and there are various tools to do that.
>>
>> The bigger problem is, even if you accomplish what you seek in terms of
>> the technical setup, it's physically unrealistic. As Mark noted, you
>> have an unsatisfied valence at the C-terminus of each residue at each
>> interval of time. This is not physically real, as amino acids are simply
>> transferred between tRNA and onto the growing polypeptide chain. Simply
>> "growing" residues onto the chain will not come close to mimicking
>> protein synthesis in any meaningful way.
>>
>> -Justin
>>
>>> Thank you and best regards,
>>> Quyen
>>>
>>> On Sat, Oct 20, 2018 at 6:27 AM Quyen Vu Van <vuqv.phys at gmail.com>
>> wrote:
>>>> Dear Mark,
>>>> I mean that e.g my protein has 10 residues in pdb file but at t=0,
>> Gromacs
>>>> will only calculate the interactions of all atoms in residue 1
>>>> t= 1ns (for example) Gromacs will calculate the interactions of all
>> atoms
>>>> in residues 1 and 2, and so on till t= XXX ns, interactions of all
>> atoms of
>>>> full protein is take into account.
>>>> Best regards,
>>>> Quyen
>>>>
>>>>
>>>> On Fri, Oct 19, 2018, 18:42 Mark Abraham <mark.j.abraham at gmail.com>
>> wrote:
>>>>> Hi,
>>>>>
>>>>> What do you mean by turning a residue off? What would terminate the
>>>>> chemical bond to the residue that it was bound to?
>>>>>
>>>>> Mark
>>>>>
>>>>> On Fri, Oct 19, 2018, 14:40 Quyen Vu Van <vuqv.phys at gmail.com> wrote:
>>>>>
>>>>>> Dear Gromacs community,
>>>>>> How can I turn off/on residues in the protein, I want to mimic the
>>>>> process
>>>>>> of protein synthesis.
>>>>>> Thank you and best regards,
>>>>>> Quyen
>>>>>> --
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>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================
>>
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================