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
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