[gmx-users] -inter command

Justin Lemkul jalemkul at vt.edu
Sun Jan 21 16:39:48 CET 2018

On 1/20/18 2:26 AM, zaved at tezu.ernet.in wrote:
>>>>>> 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?

People who have done this use their own custom versions of whatever they 
choose. Look in the literature; this feature is not officially supported 



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


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