[gmx-users] CMAP format on GROMACS

Wed Jan 8 16:26:07 CET 2020

Thanks for your input, Justin. Helpful as always.

I am assuming the array is formatted to vary phi as a function of psi
i.e. (-180,-180), (-180,-165), (-180,-150) [considering (phi,psi)] and
again but for phi = -165.

I am also assuming that, since it is a 24x24 matrix, values will start in
phi=-180,psi=-180 but will end in phi=165, psi=165. Only a 25x25 matrix
would lead to end in phi=180,psi=180, but since they -180 and 180 are
equivalent, maybe GROMACS already do this workaround?

The last question: are those values in kJ/mol?

Cheers!
--
Marcelo

> The \ are line continuation characters, so GROMACS is reading a 24x24
> matrix in a single array of values.
>
> The values are written for all values of phi at a given value of psi,
> i.e. writing each row of the matrix, starting from phi = -180, psi =
> -180 until phi = 180, psi = 180.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 7 Jan 2020 11:40:30 +0900
> From: ??? <byunjy0614 at gmail.com>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] The maxwarn fatal errors
> Message-ID: <4B64C77F-360F-44CA-B051-11DF14D7F2C7 at gmail.com>
> Content-Type: text/plain;       charset=us-ascii
>
> Dear everyone, Happy New year!
> I have gone through the Justin Lemku tutorial for Umbrella Sampling.
> During tutorial, When I treid to input the command line:
>   gmx grompp -f md_umbrella.mdp -c npt0.gro -t npt0.cpt -p topol.top -r
> npt0.gro -n index.ndx -o umbrella0.tpr
>
> I have met two warnings and they occured fatal error.:
>   Fatal error:
>   Too many warnings (2).
>    If you are sure all warnings are harmless, use the -maxwarn option.
>
> And the waring is:
>  WARNING 1 [file topol.top, line 56]:
>   The GROMOS force fields have been parametrized with a physically
>   incorrect multiple-time-stepping scheme for a twin-range cut-off. When
>   used with a single-range cut-off (or a correct Trotter
>   multiple-time-stepping scheme), physical properties, such as the density,
>   might differ from the intended values. Since there are researchers
>   actively working on validating GROMOS with modern integrators we have not
>   yet removed the GROMOS force fields, but you should be aware of these
>   issues and check if molecules in your system are affected before
>   proceeding. Further information is available at
>   https://redmine.gromacs.org/issues/2884 , and a longer explanation of
> our
>   decision to remove physically incorrect algorithms can be found at
>   https://doi.org/10.26434/chemrxiv.11474583.v1 .
>
>
> WARNING 2 [file md_umbrella.mdp]:
>   With Nose-Hoover T-coupling and Parrinello-Rahman p-coupling, tau-p (1)
>   should be at least twice as large as tau-t (1) to avoid resonances
>
> I solved this problem with using -maxwarn option but I am wondering
> whether thses warning is passed over.
> What do you think what I happend? dears. Any idea on what caused this
> problem?
>
> ------------------------------
>
> Message: 5
> Date: Mon, 6 Jan 2020 21:41:28 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] The maxwarn fatal errors
> Message-ID: <89785204-b49e-4f0c-3da9-10abd0b13d1c at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 1/6/20 9:40 PM, ??? wrote:
> > Dear everyone, Happy New year!
> > I have gone through the Justin Lemku tutorial for Umbrella Sampling.
> During tutorial, When I treid to input the command line:
> >    gmx grompp -f md_umbrella.mdp -c npt0.gro -t npt0.cpt -p topol.top -r
> npt0.gro -n index.ndx -o umbrella0.tpr
> >
> > I have met two warnings and they occured fatal error.:
> >    Fatal error:
> >    Too many warnings (2).
> >     If you are sure all warnings are harmless, use the -maxwarn option.
> >
> > And the waring is:
> >   WARNING 1 [file topol.top, line 56]:
> >    The GROMOS force fields have been parametrized with a physically
> >    incorrect multiple-time-stepping scheme for a twin-range cut-off. When
> >    used with a single-range cut-off (or a correct Trotter
> >    multiple-time-stepping scheme), physical properties, such as the
> density,
> >    might differ from the intended values. Since there are researchers
> >    actively working on validating GROMOS with modern integrators we have
> not
> >    yet removed the GROMOS force fields, but you should be aware of these
> >    issues and check if molecules in your system are affected before
> >    proceeding. Further information is available at
> >    https://redmine.gromacs.org/issues/2884 , and a longer explanation
> of our
> >    decision to remove physically incorrect algorithms can be found at
> >    https://doi.org/10.26434/chemrxiv.11474583.v1 .
> >
> >
> > WARNING 2 [file md_umbrella.mdp]:
> >    With Nose-Hoover T-coupling and Parrinello-Rahman p-coupling, tau-p
> (1)
> >    should be at least twice as large as tau-t (1) to avoid resonances
> >
> > I solved this problem with using -maxwarn option but I am wondering
> whether thses warning is passed over.
> > What do you think what I happend? dears. Any idea on what caused this
> problem?
>
> The first warning is very verbose and provides you with substantial
> justification and background reading.
>
> As for the second, change tau-p to 2 as suggested. Note that I have not
> made any attempt to update the tutorials for the 2020 version, and they
> are only guaranteed to be compatible with GROMACS 2018.x versions.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
>
>
> ------------------------------
>
> --
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> End of gromacs.org_gmx-users Digest, Vol 189, Issue 13
> ******************************************************
>

-- 
--
Marcelo Depólo Polêto
Postdoctoral Researcher
BIOAGRO - Room T07
Department of General Biology - UFV
Contact: + 55 31 3612-2464