[gmx-users] Fatel error in simulated annealing
Justin A. Lemkul
jalemkul at vt.edu
Mon Sep 8 11:58:57 CEST 2008
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
> > >
> > >
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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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> --
> ========================================
>
> 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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