[gmx-users] -inter command

[Justin Lemkul]

On 1/18/18 7:02 AM, zaved at tezu.ernet.in wrote:
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>>     1. Re: -inter command (Jo?o Henriques)
>>     2. Rupture force definition (Rakesh Mishra)
>>     3. Re: Can I get the fraction of solvent accessible	surface area
>>        using "gmx sasa"? (=?ISO-8859-1?B?WkhBTkcgQ2hlbmc=?=)
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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>
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> 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

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

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