Re: [gmx-users] GMXSCRIPT: Simple checkpointed Python scripting framework for Gromacs

[Pedro Lacerda]

Yes, GromacsWrapper doesn't enforces some project structure, it's more like
a library despite its name.
GmxScript enforces some kind of project organization. As GromacsWrapper,
it's not a huge advantage over pure shell scripts, except because every
command is checkpointed and is very readable.

Cheers,
Pedro Lacerda

2016-05-07 0:06 GMT-03:00 Peter Stern :

> I guess that Pedro clearly knows that since he refers to it on his page
> and explains why his is different.
>
> Cheers,
> Peter
>
> Sent from my iPad
>
> > On May 6, 2016, at 12:22 PM, João M. Damas  wrote:
> >
> > There is already a similar project going on for a long time:
> > https://orbeckst.github.io/GromacsWrapper/
> >
> > Cheers,
> > João
> >
> > On Wed, May 4, 2016 at 3:12 AM, Pedro Lacerda 
> > wrote:
> >
> >> Installation is now working. The upload script was broken.
> >>
> >> 2016-05-03 21:50 GMT-03:00 Pedro Lacerda :
> >>
> >>> Hi Gromacs users,
> >>>
> >>> I just started to develop a scripting framework for Gromacs, it makes
> >> some
> >>> assumptions about the directory structure and command parameters. You
> >>> cannot prepare or run two different systems in the same directory and
> >>> always pass the -deffnm option to mdrun.
> >>>
> >>> It is very nice!
> >>>
> >>> Its main goal is to easy the reproduction of simulation protocols,
> >>> canonical steps used to perform and analyze a simulation. The commands
> >> are
> >>> stored in very readable and structured Python file that requires no
> >>> programming knowledge except syntax. Of course you can always extend it
> >>> with code as you need.
> >>>
> >>> As a bonus it maintain in the .gmx/ directory a checkpoint file that
> skip
> >>> previously successful commands if started again. Also there is no need
> to
> >>> source GMXRC in common cases.
> >>>
> >>>https://github.com/pslacerda/gmx
> >>>
> >>> Please make comments, suggestions and critics about GMXSCRIPT. The next
> >>> feature would be an option to generate a file that allows to reproduce
> a
> >>> simulation in any linux computer with Gromacs installed.
> >>>
> >>> (apologies for my poor English!)
> >>>
> >>> Best regards,
> >>> Pedro Lacerda
> >> --
> >> 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.
> >
> >
> >
> > --
> > João M. Damas
> > PhD Student
> > Protein Modelling Group
> > ITQB-UNL, Oeiras, Portugal
> > Tel:+351-214469613
> > --
> > 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
>
> * 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
>
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> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] GMXSCRIPT: Simple checkpointed Python scripting framework for Gromacs

[Peter Stern]

I guess that Pedro clearly knows that since he refers to it on his page and 
explains why his is different.

Cheers, 
Peter

Sent from my iPad

> On May 6, 2016, at 12:22 PM, João M. Damas  wrote:
> 
> There is already a similar project going on for a long time:
> https://orbeckst.github.io/GromacsWrapper/
> 
> Cheers,
> João
> 
> On Wed, May 4, 2016 at 3:12 AM, Pedro Lacerda 
> wrote:
> 
>> Installation is now working. The upload script was broken.
>> 
>> 2016-05-03 21:50 GMT-03:00 Pedro Lacerda :
>> 
>>> Hi Gromacs users,
>>> 
>>> I just started to develop a scripting framework for Gromacs, it makes
>> some
>>> assumptions about the directory structure and command parameters. You
>>> cannot prepare or run two different systems in the same directory and
>>> always pass the -deffnm option to mdrun.
>>> 
>>> It is very nice!
>>> 
>>> Its main goal is to easy the reproduction of simulation protocols,
>>> canonical steps used to perform and analyze a simulation. The commands
>> are
>>> stored in very readable and structured Python file that requires no
>>> programming knowledge except syntax. Of course you can always extend it
>>> with code as you need.
>>> 
>>> As a bonus it maintain in the .gmx/ directory a checkpoint file that skip
>>> previously successful commands if started again. Also there is no need to
>>> source GMXRC in common cases.
>>> 
>>>https://github.com/pslacerda/gmx
>>> 
>>> Please make comments, suggestions and critics about GMXSCRIPT. The next
>>> feature would be an option to generate a file that allows to reproduce a
>>> simulation in any linux computer with Gromacs installed.
>>> 
>>> (apologies for my poor English!)
>>> 
>>> Best regards,
>>> Pedro Lacerda
>> --
>> 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.
> 
> 
> 
> -- 
> João M. Damas
> PhD Student
> Protein Modelling Group
> ITQB-UNL, Oeiras, Portugal
> Tel:+351-214469613
> -- 
> 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.
-- 
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Re: [gmx-users] GMXSCRIPT: Simple checkpointed Python scripting framework for Gromacs

[João M . Damas]

There is already a similar project going on for a long time:
https://orbeckst.github.io/GromacsWrapper/

Cheers,
João

On Wed, May 4, 2016 at 3:12 AM, Pedro Lacerda 
wrote:

> Installation is now working. The upload script was broken.
>
> 2016-05-03 21:50 GMT-03:00 Pedro Lacerda :
>
> > Hi Gromacs users,
> >
> > I just started to develop a scripting framework for Gromacs, it makes
> some
> > assumptions about the directory structure and command parameters. You
> > cannot prepare or run two different systems in the same directory and
> > always pass the -deffnm option to mdrun.
> >
> > It is very nice!
> >
> > Its main goal is to easy the reproduction of simulation protocols,
> > canonical steps used to perform and analyze a simulation. The commands
> are
> > stored in very readable and structured Python file that requires no
> > programming knowledge except syntax. Of course you can always extend it
> > with code as you need.
> >
> > As a bonus it maintain in the .gmx/ directory a checkpoint file that skip
> > previously successful commands if started again. Also there is no need to
> > source GMXRC in common cases.
> >
> > https://github.com/pslacerda/gmx
> >
> > Please make comments, suggestions and critics about GMXSCRIPT. The next
> > feature would be an option to generate a file that allows to reproduce a
> > simulation in any linux computer with Gromacs installed.
> >
> > (apologies for my poor English!)
> >
> > Best regards,
> > Pedro Lacerda
> >
> --
> 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.
>



-- 
João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
Tel:+351-214469613
-- 
Gromacs Users mailing list

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Re: [gmx-users] GMXSCRIPT: Simple checkpointed Python scripting framework for Gromacs

[Pedro Lacerda]

Installation is now working. The upload script was broken.

2016-05-03 21:50 GMT-03:00 Pedro Lacerda :

> Hi Gromacs users,
>
> I just started to develop a scripting framework for Gromacs, it makes some
> assumptions about the directory structure and command parameters. You
> cannot prepare or run two different systems in the same directory and
> always pass the -deffnm option to mdrun.
>
> It is very nice!
>
> Its main goal is to easy the reproduction of simulation protocols,
> canonical steps used to perform and analyze a simulation. The commands are
> stored in very readable and structured Python file that requires no
> programming knowledge except syntax. Of course you can always extend it
> with code as you need.
>
> As a bonus it maintain in the .gmx/ directory a checkpoint file that skip
> previously successful commands if started again. Also there is no need to
> source GMXRC in common cases.
>
> https://github.com/pslacerda/gmx
>
> Please make comments, suggestions and critics about GMXSCRIPT. The next
> feature would be an option to generate a file that allows to reproduce a
> simulation in any linux computer with Gromacs installed.
>
> (apologies for my poor English!)
>
> Best regards,
> Pedro Lacerda
>
-- 
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

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[gmx-users] GMXSCRIPT: Simple checkpointed Python scripting framework for Gromacs

[Pedro Lacerda]

Hi Gromacs users,

I just started to develop a scripting framework for Gromacs, it makes some
assumptions about the directory structure and command parameters. You
cannot prepare or run two different systems in the same directory and
always pass the -deffnm option to mdrun.

It is very nice!

Its main goal is to easy the reproduction of simulation protocols,
canonical steps used to perform and analyze a simulation. The commands are
stored in very readable and structured Python file that requires no
programming knowledge except syntax. Of course you can always extend it
with code as you need.

As a bonus it maintain in the .gmx/ directory a checkpoint file that skip
previously successful commands if started again. Also there is no need to
source GMXRC in common cases.

https://github.com/pslacerda/gmx

Please make comments, suggestions and critics about GMXSCRIPT. The next
feature would be an option to generate a file that allows to reproduce a
simulation in any linux computer with Gromacs installed.

(apologies for my poor English!)

Best regards,
Pedro Lacerda
-- 
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
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