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!
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>
> 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
>
> _______________________________________________
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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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