[gmx-users] Fatel error in simulated annealing
Justin A. Lemkul
jalemkul at vt.edu
Mon Sep 8 17:27:38 CEST 2008
ravi sharma wrote:
> Hello justin,
>
> whether i do correct my md.mdp by vi editor but still it was giving
> error well i removed all those groups which coupling to thermostat now
> its working (NA+ HEME SOL)
>
I guess I hadn't even considered that. If you're doing simulated annealing, and
progressively changing the temperature, you probably shouldn't be trying to
constrain the elements of your system to a single temperature!
-Justin
(Please remember to keep discussions on the gmx-users list, for example, using
"Reply All" so that the discussion may be archived for the benefit of future users)
>
> Thanks,
>
>
> Ravi Datta Sharma
> Lecturer,
> Bioinformatics,
> Department of Microbiology,
> CCS Unversity,
> Meerut
>
>
>
> --- On *Mon, 8/9/08, Justin A. Lemkul /<jalemkul at vt.edu>/* wrote:
>
> From: Justin A. Lemkul <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Fatel error in simulated annealing
> To: "Gromacs Users' List" <gmx-users at gromacs.org>
> Date: Monday, 8 September, 2008, 5:00 PM
>
> ravi sharma wrote:
> > hi
> >
> > you have written that in my file there are some trailing characters,
> > how can identify these characters ??
>
> You can see them in the vi editor.
>
> -Justin
>
> > ;simulated annealing
> > > annealing = single^M
> > > annealing_npoints = 5 ^M
> > > annealing_time = 2 500 1000 1500 2000^M
> > > annealing_temp = 300 350 400 450 450^M
> >
> >
> >
> >
> > --- On *Mon, 8/9/08, Justin A. Lemkul /<jalemkul at vt.edu>/* wrote:
> >
> > From: Justin A. Lemkul <jalemkul at vt.edu>
> > Subject: Re: [gmx-users] Fatel error in simulated annealing
> > To: "Gromacs Users' List" <gmx-users at gromacs.org>
> > Date: Monday, 8 September, 2008, 3:28 PM
> >
> >
> > ravi sharma wrote:
> > > Thanks justin,
> > >
> > > but how can identify these groups, i am using fedora core 8,
> > > also Thanks for the Tc-grps,
> > >
> > >
> >
> > What groups are you talking about, tc-grps? Please be more specific.
> >
> > -Justin
> >
> > >
> > > regards,
> > >
> > >
> > >
> > >
> > >
> > > --- On *Sun, 7/9/08, Justin A. Lemkul /<jalemkul at vt.edu>/*
> wrote:
> > >
> > > From: Justin A. Lemkul <jalemkul at vt.edu>
> > > Subject: Re: [gmx-users] Fatel error in simulated annealing
> > > To: "Discussion list for GROMACS users"
> > <gmx-users at gromacs.org>
> > > Date: Sunday, 7
> > September, 2008, 10:28 PM
> > >
> > > You have trailing characters in your simulated annealing
> section:
> > >
> > > What shows up for me is:
> > >
> > > ;simulated annealing
> > > annealing = single^M
> > > annealing_npoints = 5 ^M
> > > annealing_time = 2 500 1000 1500 2000^M
> > > annealing_temp = 300 350 400 450 450^M
> > >
> > > Are you transferring between Windows and Linux/Mac/etc.
> systems? If
> > so, you
> > > will need to process your .mdp file with dos2unix.
> > >
> > > Unsolicited advice on T-coupling:
> > >
> > > tc-grps = Protein SOL HEM NA+
> > >
> > > It's a bad idea to couple solvent, ions, and small
> molecules all
> > in
> > > different
> > > tc-grps. Reference here for information regarding
> thermostats:
> > >
> > > http://wiki.gromacs.org/index.php/thermostats
> > >
> > > -Justin
> > >
> > >
> > ravi sharma wrote:
> > > > Hello guys,
> > > > i am doing a simulation with simulated annealing of a
> > > protein which
> > > > contains heme inside,
> > > > the normal without simulated annealing its running fine
> but while
> > m
> > > > writing simulated annealing in my md.mdp its showing
> error
> > > >
> > > > //Fatal error:
> > > > Not enough annealing values: 1 (for 4 groups)
> > > >
> > > >
> > > >
> <http://www.gromacs.org/mailman/listinfo/gmx-users>//
> > > >
> > > > I am attaching my md.mdp file here
> > > >
> > > >
> > > >
> > > >
> > > > md.mdp
> > > >
> > > >
> > > >
> > > > Thanks
> > > >
> > > >
> > > > Ravi Datta Sharma
> > > > Lecturer,
> > > > Bioinformatics,
> > >
> > > Department of Microbiology,
> > > > CCS Unversity,
> > > > Meerut
> > > >
>
> > > >
> > > >
> > > > --- On *Sun, 7/9/08, Florian Dommert
> > > /<dommert at fias.uni-frankfurt.de>/*
> > > > wrote:
> > > >
> > > > From: Florian Dommert
> <dommert at fias.uni-frankfurt.de>
> > > > Subject: Re:
> > > [gmx-users] trr file format
> > > > To: "Discussion list for GROMACS users"
> > > <gmx-users at gromacs.org>
> > > > Date: Sunday, 7 September, 2008, 4:54 PM
> > > >
> > > > On 06.09.2008, at 22:28, Vitaly Chaban wrote:
> > > >
> > > > > Hello,
> > > > >
> > > > > Where can I read about the exact format of the
> TRR and
> > XTC files.
> > > I
> > > > >
> > mean the width and type of every field in the binary
> > trajectory
> > > file.
> > > > >
> > > > > I see read_'next_frame(status,&fr)'
> function
> > in
> > > > 'template.c'. But
> > > > > where is this fuction defined?
> > > > > Sorry, I'm not an expert in C. :(
> > > > >
> > > >
> > > > Hello,
> > > >
> > > > if you have problems, finding appropiate header
> files for the
> >
> > > > functions of gmx, you can perhaps use a development
> > environment like
> >
> > > Eclipse, Source-Navigator, KDevelop, Anjuta
> depending on your
> > > flavour
> > >
> > > > and operating system.
> > > > This programs index all the functions in a specified
> project
> > and you
> > > > can look up their definitions by request without
> searching
> > the files
> >
> > > > of the complete src-code.
> > > > It is hard to rank the different programs due to
> their
> > various
> > > > capabilities and your
> > > > requirements.
> > > > Eclipse Ganymed is a special C/C++ Development
> environment
> > and
> > > > accesible for every OS. Furthermore it is modular
> and you can
> > also
> > > > advance it to a
> MATLAB-like enviroment including the
> PyDev
> > module and
> > >
> > > > using python modules like numpy and scipy. It is
> also capable
> > of
> > > > accesing CVS trees directly. In my opinion this
> program
> > package is
> > > > flexible and helpful. Once everything is installed
> and
> > configured it
> > > > can be handled very easily.
> > > > The other mentioned packages are
> > > Red-Hat, KDE, and GNOME development
> > > >
> > environments. However as I mentioned at the end it is a
> > question of
> > > > flavor.
> > > >
> > > > Best Regards,
> > > >
> > > > Flo
> > > >
> > > >
> >
> > > > Thanks.
> > > > >
> > > > > --
> > > > > Vitaly V. Chaban
> > > > > School of Chemistry
> > > > > National University of Kharkiv
> > > > > Svoboda sq.,4, Kharkiv 61077, Ukraine
> > > > > email: chaban at univer.kharkov.ua
> > > > > skype: vvchaban
> > > > >
> > > > >
> > > > _______________________________________________
> > > > > gmx-users mailing list gmx-users at gromacs.org
> > > > >
> http://www.gromacs.org/mailman/listinfo/gmx-users
> > > > > Please search the archive
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> > > >
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> > > > >
> > > >
> > > > --
> > > > Florian Dommert
> > > > Dipl.-Phys.
> > > >
> > > > Computational and Theoretical Softmatter &
> Biophysics
> > group
> > > >
> > > > Frankfurt Institute for Advanced Studies
> > > > Johann-Wolfgang-Goethe University
> > > >
> > > > Ruth-Moufang-Str. 1
> > > > 60438
> Frankfurt am Main
> > > >
> > > > Phone: +49(0)69 / 798 - 47522
> > > > Fax:
> > +49(0)69 / 798 - 47611
> > > >
> > > > EMail: dommert at fias.uni-frankfurt.de
> > > > Home:
> > > >
> http://fias.uni-frankfurt.de/~simbio/Florian_Dommert
> > > >
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> >
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> > > --
> > >
> > ========================================
> > >
> > > Justin A. Lemkul
> > > Graduate Research Assistant
> > > Department of Biochemistry
> > > Virginia Tech
> > > Blacksburg, VA
> > > jalemkul[at]vt.edu | (540) 231-9080
> > >
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> > >
> > > ========================================
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> > --
> > ========================================
> >
> > Justin A. Lemkul
> > Graduate Research Assistant
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
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> --
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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