[gmx-users] Dihedral restraints

[ABEL Stephane]

Thank you Mark, 

With your example, I have finally resolved my problem and finally found that the dihedral restraints were not actived in my simulations :((
 
If someone is interested to know how I did for resolving my problem especially when you use  the files generated by CHARMM-GUI for GROMACS, do not hesitate to contact me directly

Thanks again

Stéphane

----------------------------------------------------------------------

Message: 1
Date: Thu, 10 Jan 2019 07:20:26 +0100
From: Mark Abraham <mark.j.abraham at gmail.com>
To: gmx-users at gromacs.org
Cc: "gromacs.org_gmx-users at maillist.sys.kth.se"
        <gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: Re: [gmx-users] Dihedral restraints
Message-ID:
        <CAMNuMATrH0Hv4PpgujPSmf0gnQ8WUBSGt9H=6UkuiCpCrNfLXg at mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"

Hi,

You can see a working example at

https://github.com/gromacs/regressiontests/blob/master/freeenergy/restraints/reference_s.log

so I conclude that your restraints are inactive, somehow. Please check your
include statements, etc.

Mark


On Wed., 9 Jan. 2019, 18:05 ABEL Stephane, <Stephane.ABEL at cea.fr> wrote:

> Thanks Mark for your reply
>
> In the log and edr files I only see an "Position Rest." term. So do you
> mean that the contributions on the dihedral restrains is added in in total
> energy without additional terms in the energy output in log file and the
> edr ?
>
> Thank you in advance for the clarification.
>
> St?phane
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 9 Jan 2019 12:32:31 +0100
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org
> Cc: "gromacs.org_gmx-users at maillist.sys.kth.se"
>         <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: Re: [gmx-users] Dihedral restraints
> Message-ID:
>         <CAMNuMATC-w54oR=
> XV8qBiC+t1H1cWwcNKiSdfXnOja7XBOTyZQ at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi,
>
> IIRC that's enough, for dihedral restraints. You will see energy
> contributions from the the restraints appear in your .log and .edr files if
> the restraints are active. I don't recall if there is anything printed by
> mdrun before the simulation commences.
>
> Mark
>
> On Wed, Jan 9, 2019 at 10:14 AM ABEL Stephane <Stephane.ABEL at cea.fr>
> wrote:
>
> > Hello
> >
> > I would like to apply some dihedral restraints in different residues of
> my
> > protein during the production stage. For that I have added at the end of
> > the protein itp the section
> > [ dihedral_restraints ]. Is it enough ? Should I add something else in
> the
> > mdp ?  In other words, how to be sure that the restraints are effectively
> > applied during the run ?
> >
> > I am using GROMACS 2018.2
> >
> > Thank in advance and happy new year to all
> >
> > St?phane
> > --
> --
> 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-request at gromacs.org.
>


------------------------------

Message: 2
Date: Thu, 10 Jan 2019 07:20:26 +0100
From: Mark Abraham <mark.j.abraham at gmail.com>
To: gmx-users at gromacs.org
Cc: "gromacs.org_gmx-users at maillist.sys.kth.se"
        <gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: Re: [gmx-users] Dihedral restraints
Message-ID:
        <CAMNuMATrH0Hv4PpgujPSmf0gnQ8WUBSGt9H=6UkuiCpCrNfLXg at mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"

Hi,

You can see a working example at

https://github.com/gromacs/regressiontests/blob/master/freeenergy/restraints/reference_s.log

so I conclude that your restraints are inactive, somehow. Please check your
include statements, etc.

Mark


On Wed., 9 Jan. 2019, 18:05 ABEL Stephane, <Stephane.ABEL at cea.fr> wrote:

> Thanks Mark for your reply
>
> In the log and edr files I only see an "Position Rest." term. So do you
> mean that the contributions on the dihedral restrains is added in in total
> energy without additional terms in the energy output in log file and the
> edr ?
>
> Thank you in advance for the clarification.
>
> St?phane
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 9 Jan 2019 12:32:31 +0100
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org
> Cc: "gromacs.org_gmx-users at maillist.sys.kth.se"
>         <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: Re: [gmx-users] Dihedral restraints
> Message-ID:
>         <CAMNuMATC-w54oR=
> XV8qBiC+t1H1cWwcNKiSdfXnOja7XBOTyZQ at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi,
>
> IIRC that's enough, for dihedral restraints. You will see energy
> contributions from the the restraints appear in your .log and .edr files if
> the restraints are active. I don't recall if there is anything printed by
> mdrun before the simulation commences.
>
> Mark
>
> On Wed, Jan 9, 2019 at 10:14 AM ABEL Stephane <Stephane.ABEL at cea.fr>
> wrote:
>
> > Hello
> >
> > I would like to apply some dihedral restraints in different residues of
> my
> > protein during the production stage. For that I have added at the end of
> > the protein itp the section
> > [ dihedral_restraints ]. Is it enough ? Should I add something else in
> the
> > mdp ?  In other words, how to be sure that the restraints are effectively
> > applied during the run ?
> >
> > I am using GROMACS 2018.2
> >
> > Thank in advance and happy new year to all
> >
> > St?phane
> > --
> --
> 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-request at gromacs.org.
>