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:
>>>>> 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:
>>>>>
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/pl
> 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;
-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:
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:
>
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
-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
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
