Am I using the right version for accelerated MD?

From: patrick wintrode (pat_wde2_at_yahoo.com)
Date: Tue Mar 22 2011 - 15:34:29 CDT

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

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:23:42 CST