Re: [gmx-users] Possible to extract gro file from a tpr?

[Mark Abraham]

Hi,

As Justin observed, editconf -f your.tpr -o your.pdb just works.

Mark
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Re: [gmx-users] Possible to extract gro file from a tpr?

[Mark Abraham]

We haven't yet moved to Discourse ;-)

On Tue, Apr 3, 2018, 10:54 Viveca Lindahl  wrote:

> Wish I could +1 the best response here :) Thanks.
>
> --
> Viveca
>
>
> On Fri, Mar 30, 2018 at 8:35 PM, Mark Abraham 
> wrote:
>
> > Just say No! :-)
> >
> > On Fri, Mar 30, 2018, 19:58 Alex  wrote:
> >
> > > Or, and that is a very peculiar option, genion with -conc 0. :)
> > >
> > > Alex
> > >
> > >
> > > On 3/30/2018 4:28 AM, Justin Lemkul wrote:
> > > > On Fri, Mar 30, 2018 at 5:38 AM Viveca Lindahl <
> > vivecalind...@gmail.com>
> > > > wrote:
> > > >
> > > >> Hi users,
> > > >>
> > > >> Is it possible to extract a gro file from a tpr?  Unfortunately 'gmx
> > > mdrun
> > > >> -nsteps 0' does not give a confout.gro :)
> > > >>
> > > > Just use editconf.
> > > >
> > > > -Justin
> > > >
> > > >
> > > >> --
> > > >> Viveca
> > > >> --
> > > >> 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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> > > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > >> send a mail to gmx-users-requ...@gromacs.org.
> > > >>
> > >
> > > --
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[gmx-users] Possible to extract gro file from a tpr?

[ABEL Stephane]

Hi 

A quick question here, before to read this response I thought (but never 
tested) that it was possible to extract a pdb from a tpr since we use one to 
generate a tpr with grompp. So how is store the atomic coordinates of a system 
in a tpr file ?

Thanks  

--

Message: 1
Date: Tue, 3 Apr 2018 10:54:09 +0200
From: Viveca Lindahl <vivecalind...@gmail.com>
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Possible to extract gro file from a tpr?
Message-ID:

Re: [gmx-users] Possible to extract gro file from a tpr?

[Viveca Lindahl]

Wish I could +1 the best response here :) Thanks.

--
Viveca


On Fri, Mar 30, 2018 at 8:35 PM, Mark Abraham 
wrote:

> Just say No! :-)
>
> On Fri, Mar 30, 2018, 19:58 Alex  wrote:
>
> > Or, and that is a very peculiar option, genion with -conc 0. :)
> >
> > Alex
> >
> >
> > On 3/30/2018 4:28 AM, Justin Lemkul wrote:
> > > On Fri, Mar 30, 2018 at 5:38 AM Viveca Lindahl <
> vivecalind...@gmail.com>
> > > wrote:
> > >
> > >> Hi users,
> > >>
> > >> Is it possible to extract a gro file from a tpr?  Unfortunately 'gmx
> > mdrun
> > >> -nsteps 0' does not give a confout.gro :)
> > >>
> > > Just use editconf.
> > >
> > > -Justin
> > >
> > >
> > >> --
> > >> Viveca
> > >> --
> > >> Gromacs Users mailing list
> > >>
> > >> * Please search the archive at
> > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > >> posting!
> > >>
> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >>
> > >> * For (un)subscribe requests visit
> > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > >> send a mail to gmx-users-requ...@gromacs.org.
> > >>
> >
> > --
> > Gromacs Users mailing list
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> > posting!
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> >
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Re: [gmx-users] Possible to extract gro file from a tpr?

[Mark Abraham]

Just say No! :-)

On Fri, Mar 30, 2018, 19:58 Alex  wrote:

> Or, and that is a very peculiar option, genion with -conc 0. :)
>
> Alex
>
>
> On 3/30/2018 4:28 AM, Justin Lemkul wrote:
> > On Fri, Mar 30, 2018 at 5:38 AM Viveca Lindahl 
> > wrote:
> >
> >> Hi users,
> >>
> >> Is it possible to extract a gro file from a tpr?  Unfortunately 'gmx
> mdrun
> >> -nsteps 0' does not give a confout.gro :)
> >>
> > Just use editconf.
> >
> > -Justin
> >
> >
> >> --
> >> Viveca
> >> --
> >> 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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> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-requ...@gromacs.org.
> >>
>
> --
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Re: [gmx-users] Possible to extract gro file from a tpr?

[Alex]

Or, and that is a very peculiar option, genion with -conc 0. :)

Alex


On 3/30/2018 4:28 AM, Justin Lemkul wrote:

On Fri, Mar 30, 2018 at 5:38 AM Viveca Lindahl 
wrote:


Hi users,

Is it possible to extract a gro file from a tpr?  Unfortunately 'gmx mdrun
-nsteps 0' does not give a confout.gro :)


Just use editconf.

-Justin



--
Viveca
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Re: [gmx-users] Possible to extract gro file from a tpr?

[Justin Lemkul]

On Fri, Mar 30, 2018 at 5:38 AM Viveca Lindahl 
wrote:

> Hi users,
>
> Is it possible to extract a gro file from a tpr?  Unfortunately 'gmx mdrun
> -nsteps 0' does not give a confout.gro :)
>

Just use editconf.

-Justin


> --
> Viveca
> --
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-- 

==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441


==
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Re: [gmx-users] Possible to extract gro file from a tpr?

[Gregory Man Kai Poon]

Hi Viveca,

You could specify in trjconv to output a gro file:

gmx trjconv -s md.tpr -f md.xtc -o md.gro ...

Would that work?

Gregory

Get Outlook for Android<https://aka.ms/ghei36>



From: Viveca Lindahl
Sent: Friday, March 30, 5:38 AM
Subject: [gmx-users] Possible to extract gro file from a tpr?
To: gmx-us...@gromacs.org


Hi users, Is it possible to extract a gro file from a tpr? Unfortunately 'gmx 
mdrun -nsteps 0' does not give a confout.gro :) -- Viveca -- Gromacs Users 
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[gmx-users] Possible to extract gro file from a tpr?

[Viveca Lindahl]

Hi users,

Is it possible to extract a gro file from a tpr?  Unfortunately 'gmx mdrun
-nsteps 0' does not give a confout.gro :)

--
Viveca
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