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
>
>
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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: [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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