[gmx-users] Fatel error in simulated annealing

Justin A. Lemkul jalemkul at vt.edu
Mon Sep 8 13:30:08 CEST 2008



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 /<jalemkul at vt.edu>/* wrote:
> 
>     From: Justin A. Lemkul <jalemkul at vt.edu>
>     Subject: Re: [gmx-users] Fatel error in simulated annealing
>     To: "Gromacs Users' List" <gmx-users at 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 /<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
>     >     >     >
>     >     >     >
>     >     >      _______________________________________________
>     >     >     > 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
>     > 
>     >     ========================================
>     >     _______________________________________________
>     >     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
>     > 
>     > 
>     >
>      ------------------------------------------------------------------------
>     > Download prohibited? No problem. CHAT 
>     >
>     <http://in.rd.yahoo.com/tagline_webmessenger_1/*http://in.webmessenger.yahoo.com/>
> 
>     > from any browser, without download.
> 
>     -- 
>     ========================================
> 
>     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 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/> 
> 

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

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

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



More information about the gromacs.org_gmx-users mailing list