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

[Quyen Vu Van]

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
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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>