Re: Am I using the right version for accelerated MD?

From: Chris Harrison (charris5_at_gmail.com)
Date: Tue Mar 22 2011 - 16:11:35 CDT

Dear Patrick,

It looks like there is a typo in the manual. Instead of accelMDOn, you
should be using:
accelMD on

I believe this will fix your error. Can you retry and let us know?

Best,
Chris

--
Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
char_at_ks.uiuc.edu                          Voice: 217-244-1733
http://www.ks.uiuc.edu/~char              Fax:   217-244-6078
patrick wintrode <pat_wde2_at_yahoo.com> writes:
> Date: Tue, 22 Mar 2011 13:34:29 -0700 (PDT)
> From: patrick wintrode <pat_wde2_at_yahoo.com>
> To: namd-l_at_ks.uiuc.edu
> Subject: namd-l: Am I using the right version for accelerated MD?
> X-Mailer: YahooMailClassic/11.4.20 YahooMailWebService/0.8.109.295617
> 
> Hi,
> 
> I am trying to use accelerated MD using the build:
> 
> NAMD CVS-2011-03-18 for Linux-x86_64
> 
> It failed to start with the following error messages:
> 
> ------------------------------------------------------------------------------------------------------------------------------------
> Warning: The following variables were set in the
> Warning: configuration file but will be ignored:
> Warning:    accelMDE (accelMD)
> Warning:    accelMDalpha (accelMD)
> Warning:    accelMDdual (accelMD)
> Warning:    accelMDTE (accelMDdual)
> Warning:    accelMDTalpha (accelMDdual)
> ERROR: The following variables were set in the
> ERROR: configuration file but are NOT VALID
> ERROR:    accelMDOn
> FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
> [0] Stack Traceback:
>   [0:0] CmiAbort+0x7b  [0xb9c6ed]
>   [0:1] _Z8NAMD_diePKc+0x62  [0x5334d2]
>   [0:2] _ZN13SimParameters22initialize_config_dataEP10ConfigListRPc+0x73  [0xa5297f]
>   [0:3] _ZN9NamdState14configListInitEP10ConfigList+0x3d9  [0x9acf47]
>   [0:4] _ZN9ScriptTcl9initcheckEv+0x5e  [0xa2a9c2]
>   [0:5] _ZN9ScriptTcl7Tcl_runEPvP10Tcl_InterpiPPc+0x1e  [0xa26d6c]
>   [0:6] TclInvokeStringCommand+0x91  [0xbd1568]
>   [0:7] /usr/local/namd/NAMD_CVS-2011-03-18_Linux-x86_64//namd2 [0xc073b8]
>   [0:8] Tcl_EvalEx+0x176  [0xc079fb]
>   [0:9] Tcl_EvalFile+0x134  [0xbff404]
>   [0:10] _ZN9ScriptTcl4loadEPc+0x10  [0xa264c2]
>   [0:11] _Z18after_backend_initiPPc+0x448  [0x537890]
>   [0:12] main+0x3a  [0x537412]
>   [0:13] __libc_start_main+0xf4  [0x303c01d994]
>   [0:14] _ZNSt8ios_base4InitD1Ev+0x4a  [0x532dca]
> ----------------------------------------------------------------------------------------------------------------------------------
> 
> The relevant portion of my configuration file is:
> 
> ----------------------------------------------------------------------------------------------------------------------------------
> # Accelerated MD parameters
> accelMDOn           on
> accelMDE            650
> accelMDalpha        105
> accelMDdual         on
> accelMDTE           650
> accelMDTalpha       105
> ----------------------------------------------------------------------------------------------------------------------------------
> 
> It looks like I've either got the syntax wrong or else I'm using the wrong version. Any advice would be helpful.
> 
> Thanks.
> 
> Patrick L. Wintrode
> Assistant Professor
> Dept. of Physiology & Biophysics
> Case Western Reserve University
> Cleveland, Ohio 44106

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