[gmx-users] -inter command

[zaved at tezu.ernet.in]

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>    1. Re: -inter command (Jo?o Henriques)
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> ----------------------------------------------------------------------
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> 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?

Thank You

Regards
Zaved

> A lot of OPs have the tendency to follow-up with private emails and I feel
> it should stay public so other people might benefit from the information
> as
> well. Here is the rest of the conversation regarding this thread.
>
> """
> Dear Zaved,
>
> I'm not aware of any tutorials for Gromacs, and Gromacs does not support
> constant-pH MD simulations straight out of the box. It must be (heavily)
> modified. Amber comes pre-packaged with constant-pH functionality, I
> believe. Still, you probably don't want to get involved in any of this. My
> comment about it was merely to make you aware that changing the
> protonation
> states by hand doesn't make mean you're really simulating at a given pH.
> Still, 99.9% of the people in this field do what you were wanting to do,
> i.e., change the protonation states during pdb2gmx to whatever they feel
> is
> more representative of that residue at a given pH and then hit run. I also
> do it, unless I'm studying something where charge regulation playes a
> major
> role, so by all means go ahead and try the simpler solution first.
>
> P.S.: Please avoid sending private messages about these subjects. It
> started in gmx-users and should stay there for several reasons. The main
> one is that other people might have the same problem and this information
> might be useful for them as well.
>
> Best regards,
> J
>
> On Tue, Jan 16, 2018 at 6:54 AM, <zaved at tezu.ernet.in> wrote:
>
>> Dear Sir
>>
>> Thank you for your kind response regarding the -inter command.
>>
>> Sir can you guide / provide any tutorial for constant-pH MD simulation
>> in
>> gromacs (eg., to perform simulation at pH 9)?
>>
>> I shall be grateful to you for the same.
>>
>> Thank You
>>
>> Regards
>> Zaved Hazarika
>> Research Scholar
>> Dept. Of Molecular Biology and Biotechnology,
>> Tezpur University,
>> Napam, 784028,
>> Assam,
>> India
>>
>>
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>
> J
>
> On Mon, Jan 15, 2018 at 11:51 AM, Jo?o Henriques <
> joao.m.a.henriques at gmail.com> wrote:
>
>> -inter sets the interactive mode for a bunch of other flags. Most are
>> used
>> for selecting the protonation states of the termini and other residues.
>> It
>> can also be used for interactive SS bridge selection.
>>
>> > "for setting the protonation state of charged amino acids in order to
>> perform simulation at different pH?"
>>
>> Please note that changing the protonation states of the residues does
>> not
>> mean you're performing the simulation at a "different pH". A proper
>> constant-pH MD simulation allows the residues to titrate in respect to
>> the
>> solution pH as well as the their "molecular environment". In this case,
>> your residues will be "stuck" in a user defined protonation state that
>> may
>> or may not reflect the most populated protonation states of those
>> residues
>> at a given pH, irrespectively of their surroundings.
>>
>> Cheers,
>> J
>>
>> On Mon, Jan 15, 2018 at 11:00 AM, <zaved at tezu.ernet.in> wrote:
>>
>>> Dear Gromacs Users
>>>
>>> I have an query regarding gmx pdb2gmx -inter command.
>>>
>>> Do we use -inter command only for setting the protonation state of
>>> charged
>>> amino acids in order to perform simulation at different pH?
>>>
>>>
>>> Thank You
>>>
>>> Regards
>>> Zaved Hazarika
>>> Research Scholar
>>> Dept. Of Molecular Biology and Biotechnology,
>>> Tezpur University,
>>> India



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