[gmx-users] Fatel error in simulated annealing

[Justin A. Lemkul]

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 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 gmx-users-request at gromacs.org.
>     > 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: dommert at fias.uni-frankfurt.de
>     Home:
>      http://fias.uni-frankfurt.de/~simbio/Florian_Dommert
> 
>     _______________________________________________
>     gmx-users mailing list    gmx-users at 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 gmx-users-request at gromacs.org.
>     Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> 
> ------------------------------------------------------------------------
> Unlimited freedom, unlimited storage. Get it now 
> <http://in.rd.yahoo.com/tagline_mail_2/*http://help.yahoo.com/l/in/yahoo/mail/yahoomail/tools/tools-08.html/> 
> 
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at 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 gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

-- 
========================================

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

========================================