[gmx-users] -inter command

[zaved at tezu.ernet.in]

>>>>> Message: 1
>>>>> Date: Tue, 16 Jan 2018 08:30:10 +0100
>>>>> From: Jo?o Henriques <joao.m.a.henriques at gmail.com>
>>>>> To: gmx-users at gromacs.org
>>>>> Subject: Re: [gmx-users] -inter command
>>>>> Message-ID:
>>>>> 	<CAHv45qOCV7fOu8heK0q1w_=GDZMEvRCXz35CT8xXzFWWNgUtiQ at mail.gmail.com>
>>>>> Content-Type: text/plain; charset="UTF-8"
>>>> Thank you so much Joao Sir for your kind response.
>>>>
>>>> 1. I have predicted the pka values for my protein using H++ server.
>>>>
>>>> 2. Based on the pka values, I have set the protonation states of the
>>>> charged residues using -inter command for pH 9.
>>>>
>>>> 3.I have run my simulation at pH 9 (keeping charge of +8e) using
>>>> gromacs
>>>> 5.1.4 and gromos54a7 ff.
>>>>
>>>> After performing 100ns simulation, I didn't observed any change
>>>> compared
>>>> to control system.
>>>>
>>>> Can you provide any advice on it?
>>> In what ways do the "pH 9" and "control" simulations differ? What do
>>> you
>>> define as "control" in this instance, default protonation by pdb2gmx?
>>> If
>>> that's the case, unless you have some very noncanonical pKa values,
>>> there's nothing that's really expected to be different between these
>>> two
>>> pH values, except perhaps the N-terminus itself.
>>>
>>> What are you trying to compare or calculate? Perhaps 100 ns is
>>> insufficient to observe whatever it is you're after. How have you
>>> quantified that there is no difference/change between these systems?
>>>
>>> -Justin
>>
>> Thank you so much Justin.
>>
>> 1. Yes you are correct. control here means default protonation state and
>> in this case the system charge of +8e is neutralized. I didn't have any
>> noncanonical pka values (at ph9). Checked with both H++ server and
>> Propka.
>> For ph 9, I have kept the charge of +8e.
>>
>> 2. Our experimental data suggests that at higher pH (9), the protein
>> initiates unfolding.
>>
>> 3. I have taken the final structure (at 100ns) of both systems and
>> superimposed it. I got a RMSD of 1.030 angstrom and no major structural
>> change was observed.
>>
>> 4. We can consider to extend the simulation to visualize any change, if
>> above things are correct.
>
> There won't be one. Since the topologies are identical, you're running
> the same simulation twice, and concluding that there are no major
> variations between the two. You don't actually have any simulation that
> you can claim is representing anything other than "pH 7," though pH
> isn't really a thing in fixed-charge/fixed-topology MD. This is a
> limitation of modeling something with fixed protonation states; it
> doesn't necessarily reflect reality. A constant pH method might show
> some results, but AFAIK this is not possible in GROMACS (though some
> people do have custom code in old versions that might work). You may
> want to consider a different program like AMBER or CHARMM that can do
> these types of simulations.
>
> -Justin

Thank You so much Justin.

Can you provide the name and any link for older gromacs version?

Thank You




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