Re: [gmx-users] -inter command

[Justin Lemkul]

On 1/20/18 2:26 AM, za...@tezu.ernet.in wrote:

Message: 1
Date: Tue, 16 Jan 2018 08:30:10 +0100
From: Jo?o Henriques <joao.m.a.henriq...@gmail.com>
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] -inter command
Message-ID:

[gmx-users] -inter command

[zaved]

>>>>> Message: 1
>>>>> Date: Tue, 16 Jan 2018 08:30:10 +0100
>>>>> From: Jo?o Henriques <joao.m.a.henriq...@gmail.com>
>>>>> To: gmx-us...@gromacs.org
>>>>> Subject: Re: [gmx-users] -inter command
>>>>> Message-ID:
>>>>>   

Re: [gmx-users] -inter command

[Justin Lemkul]

On 1/19/18 7:25 AM, za...@tezu.ernet.in wrote:

Message: 3
Date: Thu, 18 Jan 2018 07:39:39 -0500
From: Justin Lemkul <jalem...@vt.edu>
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] -inter command
Message-ID: <0281054c-c062-90c3-2243-ef0f5f3ed...@vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed



On 1/18/18 7:02 AM, za...@tezu.ernet.in wrote:

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Today's Topics:

 1. Re: -inter command (Jo?o Henriques)
 2. Rupture force definition (Rakesh Mishra)
 3. Re: Can I get the fraction of solvent accessiblesurface area
using "gmx sasa"? (=?ISO-8859-1?B?WkhBTkcgQ2hlbmc=?=)


--

Message: 1
Date: Tue, 16 Jan 2018 08:30:10 +0100
From: Jo?o Henriques <joao.m.a.henriq...@gmail.com>
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] -inter command
Message-ID:

[gmx-users] -inter command

[zaved]

> Message: 3
> Date: Thu, 18 Jan 2018 07:39:39 -0500
> From: Justin Lemkul <jalem...@vt.edu>
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] -inter command
> Message-ID: <0281054c-c062-90c3-2243-ef0f5f3ed...@vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 1/18/18 7:02 AM, za...@tezu.ernet.in wrote:
>>> Send gromacs.org_gmx-users mailing list submissions to
>>> gromacs.org_gmx-users@maillist.sys.kth.se
>>>
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>>>
>>> When replying, please edit your Subject line so it is more specific
>>> than "Re: Contents of gromacs.org_gmx-users digest..."
>>>
>>>
>>> Today's Topics:
>>>
>>> 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=?=)
>>>
>>>
>>> --
>>>
>>> Message: 1
>>> Date: Tue, 16 Jan 2018 08:30:10 +0100
>>> From: Jo?o Henriques <joao.m.a.henriq...@gmail.com>
>>> To: gmx-us...@gromacs.org
>>> Subject: Re: [gmx-users] -inter command
>>> Message-ID:
>>> 

Re: [gmx-users] -inter command

[Justin Lemkul]

On 1/18/18 7:02 AM, za...@tezu.ernet.in wrote:

Send gromacs.org_gmx-users mailing list submissions to
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https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
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gromacs.org_gmx-users-requ...@maillist.sys.kth.se

You can reach the person managing the list at
gromacs.org_gmx-users-ow...@maillist.sys.kth.se

When replying, please edit your Subject line so it is more specific
than "Re: Contents of gromacs.org_gmx-users digest..."


Today's Topics:

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=?=)


--

Message: 1
Date: Tue, 16 Jan 2018 08:30:10 +0100
From: Jo?o Henriques <joao.m.a.henriq...@gmail.com>
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] -inter command
Message-ID:

[gmx-users] -inter command

[zaved]

> Send gromacs.org_gmx-users mailing list submissions to
>   gromacs.org_gmx-users@maillist.sys.kth.se
>
> To subscribe or unsubscribe via the World Wide Web, visit
>   https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or, via email, send a message with subject or body 'help' to
>   gromacs.org_gmx-users-requ...@maillist.sys.kth.se
>
> You can reach the person managing the list at
>   gromacs.org_gmx-users-ow...@maillist.sys.kth.se
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gromacs.org_gmx-users digest..."
>
>
> Today's Topics:
>
>1. Re: -inter command (Jo?o Henriques)
>2. Rupture force definition (Rakesh Mishra)
>3. Re: Can I get the fraction of solvent accessiblesurface area
>   using "gmx sasa"? (=?ISO-8859-1?B?WkhBTkcgQ2hlbmc=?=)
>
>
> --
>
> Message: 1
> Date: Tue, 16 Jan 2018 08:30:10 +0100
> From: Jo?o Henriques <joao.m.a.henriq...@gmail.com>
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] -inter command
> Message-ID:
>   

Re: [gmx-users] -inter command

[João Henriques]

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,  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
> C/O Dr. A.N. Jha
> Dept. Of Molecular Biology and Biotechnology,
> Tezpur University,
> Napam, 784028,
> Assam,
> India
>
>
> * * * D I S C L A I M E R * * *
> This e-mail may contain privileged information and is intended solely for
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> disseminate, distribute or copy this e-mail. Please notify the sender
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> delayed, or may contain viruses. The recipient must verify the integrity of
> this e-mail message.

"""

J

On Mon, Jan 15, 2018 at 11:51 AM, João Henriques <
joao.m.a.henriq...@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,  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
>>
>>
>> * * * D I S C L A I M E R * * *
>> This e-mail may contain privileged information and is intended solely for
>> the individual named. If you are not the named addressee you should not
>> disseminate, distribute or copy this e-mail. Please notify the sender
>> immediately by e-mail if you have received this e-mail in error and destroy
>> it from your system. Though considerable effort has been made to deliver
>> error free e-mail messages but it can not be guaranteed to be secure or
>> error-free as information could be intercepted, corrupted, lost, destroyed,
>> delayed, or may contain viruses. The recipient must verify the integrity of
>> this e-mail message.
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
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>>
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>> send a mail to gmx-users-requ...@gromacs.org.
>>
>
>
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* Please search the archive at 

Re: [gmx-users] -inter command

[João Henriques]

-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,  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
>
>
> * * * D I S C L A I M E R * * *
> This e-mail may contain privileged information and is intended solely for
> the individual named. If you are not the named addressee you should not
> disseminate, distribute or copy this e-mail. Please notify the sender
> immediately by e-mail if you have received this e-mail in error and destroy
> it from your system. Though considerable effort has been made to deliver
> error free e-mail messages but it can not be guaranteed to be secure or
> error-free as information could be intercepted, corrupted, lost, destroyed,
> delayed, or may contain viruses. The recipient must verify the integrity of
> this e-mail message.
> --
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>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
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[gmx-users] -inter command

[zaved]

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


* * * D I S C L A I M E R * * *
This e-mail may contain privileged information and is intended solely for the 
individual named. If you are not the named addressee you should not 
disseminate, distribute or copy this e-mail. Please notify the sender 
immediately by e-mail if you have received this e-mail in error and destroy it 
from your system. Though considerable effort has been made to deliver error 
free e-mail messages but it can not be guaranteed to be secure or error-free as 
information could be intercepted, corrupted, lost, destroyed, delayed, or may 
contain viruses. The recipient must verify the integrity of this e-mail message.
-- 
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