Thanks,
Ravi Datta Sharma
Lecturer,
Bioinformatics,
Department of Microbiology,
CCS Unversity,
Meerut
--- On *Mon, 8/9/08, Justin A. Lemkul /<[EMAIL PROTECTED]>/* wrote:
From: Justin A. Lemkul <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] Fatel error in simulated annealing
To: "Gromacs Users' List" <gmx-users@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 /<[EMAIL PROTECTED]>/* wrote:
>
> From: Justin A. Lemkul <[EMAIL PROTECTED]>
> Subject: Re: [gmx-users] Fatel error in simulated annealing
> To: "Gromacs Users' List" <gmx-users@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 /<[EMAIL PROTECTED]>/*
wrote:
> >
> > From: Justin A. Lemkul <[EMAIL PROTECTED]>
> > Subject: Re: [gmx-users] Fatel error in simulated annealing
> > To: "Discussion list for GROMACS users"
> <gmx-users@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
> > /<[EMAIL PROTECTED]>/*
> > > wrote:
> > >
> > > From: Florian Dommert
<[EMAIL PROTECTED]>
> > > Subject: Re:
> > [gmx-users] trr file format
> > > To: "Discussion list for GROMACS users"
> > <gmx-users@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: [EMAIL PROTECTED]
> > > > skype: vvchaban
> > > >
> > > >
> > > _______________________________________________
> > > > gmx-users mailing list gmx-users@gromacs.org
> > > >
http://www.gromacs.org/mailman/listinfo/gmx-users
> > > > Please search the archive
> at
> http://www.gromacs.org/search before
> >
> > >
> posting!
> > > > Please don't post (un)subscribe requests to
the
> list. Use the
> > >
> > > www interface or send it to
[EMAIL PROTECTED]
> > > > Can't post? Read
> > http://www.gromacs.org/mailing_lists/users.php
> > > >
> > >
> > > --
> > > 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: [EMAIL PROTECTED]
> > > Home:
> > >
http://fias.uni-frankfurt.de/~simbio/Florian_Dommert
> > >
> > > _______________________________________________
> > > gmx-users mailing list gmx-users@gromacs.org
> > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > Please search the
> > archive at http://www.gromacs.org/search before
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> > >
> > >
> > >
>
------------------------------------------------------------------------
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> freedom, unlimited storage. Get it now
> > >
> >
>
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> >
> > >
> > >
> > >
> > >
>
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> > >
> > > _______________________________________________
> > > gmx-users mailing list
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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
> >
> > ========================================
> > _______________________________________________
> > gmx-users mailing list gmx-users@gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
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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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