VMD-L Mailing List

From: Gregorio Fernandez (gregorio_at_umh.es)
Date: Mon Apr 09 2012 - 06:21:33 CDT

Dear Bo,
Thank you very much for your mail.
I solved my problems with namd2 by moving to Linux. There is a problem
with namd2 and windows vista that I was unable to identify. My file
4ake-target_autopsf-grid.dx was not corrupted since it is actually being
used with namd2 under Linux.

Regarding the "mdff_template.namd", the file became "real" when I
launched VMD as Administrator. Running VMD as a normal user left the
file disable (I couldn't copy, edit, etc.). Once in the real world I
moved all configuration files to Linux and run namd2 without problems.

Thanks
Gregorio

El 08/04/2012 23:36, Bo Liu escribió:
>
>
> On Fri, Apr 6, 2012 at 2:42 AM, Gregorio Fernandez <gregorio_at_umh.es
> <mailto:gregorio_at_umh.es>> wrote:
>
> Hi,
> I am a very new user of VMD/MDFF. I tried to reproduce the simple
> example in the mdff tutorial by using the windows version (vmd
> 1.9.1cuda and namd2.9b2 under windows vista and also windows 7).
> I found two problems:
> 1) location of the output files. Some files can be redirected to a
> desired directory, but others cannot (i.e. mdff_template.namd).
> Where is stored that information? is a symbolic link? How can I
> get that information in a file in my directory of work?
>
> Output files of MDFF simulations can be directed to a path specified
> in your NAMD configuration file, in your case, you can modify
> adk-step1.namd file to redirect output files.
>
> mdff_template.namd is automatically generated by running "mdff setup"
> command during setting up the simulation in VMD. This file is sourced
> at the end of your NAMD configuration file, in your case, the
> adk-step1.namd file, to complete parameters that NAMD needs to perform
> an MDFF simulation. So, mdff_template.namd is not a result file but it
> is really needed to start a simulation. By default, mdff_template.namd
> is written in your current working directory, the same directory as
> your NAMD configuration file, adk-step1.namd
>
> If you know tcl scripting language well, you can check the default
> behavior of "mdff setup" command by looking at mdff_setup.tcl code in
> your VMD plugin folder (should be
> YOUR_VMD_PATH/plugins/noarch/tcl/mdff0.2/mdff_setup.tcl), around line
> 280 defines where mdff_template.namd should be written.
>
>
> 2) When running namd2 (%namd2 adk-step1.namd > adk-step1.log)(pag
> 13 of the tutorial) I got the following error: "Charm++ fatal error:
> FATAL ERROR: Grid force potential file incorrectly formatted".
> I followed the tutorial step by step. I am attaching the log file.
>
> Can you try to follow the tutorial and re-generate your file
> "4ake-target_autopsf-grid.dx" by running "mdff griddx" command?
>
> It looks like your file is corrupted.
>
>
> Best.
> Bo
>
>
> Can I have some help? Sorry if these questions are too basic.
>
> Gregorio
>
> --
> Gregorio J. Fernandez Ballester
> Instituto de Biología Molecular y Celular
> Universidad Miguel Hernández
> Edificio Torregaitán.
> Avda. de la Universidad, s/n. 03202
> Elche (Alicante)
> E-mail: gregorio_at_umh.es <mailto:gregorio_at_umh.es>
> Telf: 966 65 84 41
> Fax: 966 65 87 58
>
>
>
>
> --
> ========================================
> Bo Liu
> Theoretical and Computational Biophysics Group
> 3027 Beckman Institute
> University of Illinois at Urbana-Champaign
> 405 N. Mathews
> Urbana, IL 61801
> http://www.ks.uiuc.edu/~boliu <http://www.ks.uiuc.edu/%7Eboliu>
> ======================================== 

-- 
Gregorio J. Fernandez Ballester
Instituto de Biología Molecular y Celular
Universidad Miguel Hernández
Edificio Torregaitán.
Avda. de la Universidad, s/n. 03202
Elche (Alicante)
E-mail: gregorio_at_umh.es
Telf: 966 65 84 41
Fax:  966 65 87 58