From: Jerry Ebalunode (jebalunode_at_UH.EDU)
Date: Mon Mar 07 2005 - 14:50:20 CST
Hi all,
Since, amber parameter/structure files don't carry info on segment ids, is
there another way to specify the pulled atoms in the tclforces script file in
an smd simulution?. I already tried including a psf file built with vmd for
this but was unable to start the simulation.
here is my namd output
-----
Info: Entering startup phase 6 with 10735 kB of memory in use.
Measuring processor speeds... Done.
Info: Entering startup phase 7 with 10736 kB of memory in use.
Info: COULOMB TABLE R-SQUARED SPACING: 0.0625
Info: COULOMB TABLE SIZE: 705 POINTS
Info: NONZERO IMPRECISION IN COULOMB TABLE: 0 (0) 5.55865e-22 (656)
Info: NONZERO IMPRECISION IN COULOMB TABLE: 5.04871e-29 (651) 1.00974e-27
(633)
Info: NONZERO IMPRECISION IN COULOMB TABLE: 8.47033e-22 (693) 1.48231e-21
(697)
TCL: atom not found
FATAL ERROR: atom not found
while executing
"atomid BH 2 H4"
invoked from within
"set id1 [atomid BH 2 H4]"
(file "smd.tcl" line 3)
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: atom not found
while executing
"atomid BH 2 H4"
invoked from within
"set id1 [atomid BH 2 H4]"
(file "smd.tcl" line 3)
Stack Traceback:
[0] CmiAbort+0x48 [0x63c26f]
[1] _Z8NAMD_diePKc+0x46 [0x4907c6]
[2] _ZN15GlobalMasterTcl10initializeEv+0x36a [0x554dfa]
[3] _ZN15GlobalMasterTclC1Ev+0x43 [0x553fb3]
[4] _ZN10ComputeMgr14createComputesEP10ComputeMap+0x266 [0x4b49b6]
[5] _ZN4Node7startupEv+0x2f0 [0x5890a0]
[6] CkDeliverMessageFree+0x39 [0x605553]
[7] _Z15_processHandlerPvP11CkCoreState+0x2c5 [0x606559]
[8] CmiHandleMessage+0x28 [0x640bc4]
[9] CsdScheduleForever+0x52 [0x640cf3]
[10] CsdScheduler+0xd [0x640c83]
[11] _ZN9ScriptTcl11Tcl_measureEPvP10Tcl_InterpiPPc+0x11a [0x5b473a]
[12] TclInvokeStringCommand+0x91 [0x653658]
[13] TclExecuteByteCode+0x856 [0x66df3f]
[14] Tcl_EvalObjEx+0x2bb [0x65406b]
[15] Tcl_WhileObjCmd+0x6a [0x6607ed]
[16] namd2 [0x6894a8]
[17] Tcl_EvalEx+0x176 [0x689aeb]
[18] Tcl_EvalFile+0x134 [0x6814f4]
[19] _ZN9ScriptTcl3runEPc+0x12 [0x5b6022]
[20] main+0x1d6 [0x493016]
[21] __libc_start_main+0xa0 [0x2a95d0e0e0]
[22] cos+0x1ca [0x4900ea]
Charm++ fatal error:
FATAL ERROR: atom not found
while executing
"atomid BH 2 H4"
invoked from within
"set id1 [atomid BH 2 H4]"
(file "smd.tcl" line 3)
Aborted
-- Jerry Ebalunode RM 402F Houston Science Center Dept. of Biology and Biochemistry University of Houston 4800 Calhoun Road Houston, TX 77204 "No trees were killed in the posting of this message. However a large number of electrons were terribly inconvenienced..." Marcos Topete
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