From: Paulo Cesar Telles de Souza (paulocts_at_gmail.com)
Date: Wed Sep 02 2009 - 13:11:07 CDT
Dear Jerome
Thanks a lot for your help! I didn't know that the NAMD 2.7b1 altered ABF
method (and others) in such a way. I have decided to use this new version of
NAMD with colvars module. I don't think that it is necessary employing
multidimensional ABF for my problem. I have obtained PMF using a SMDs and
Jarzynski equality and now I would like to compare the result with one
obtained using another free energy calculation method. To specify the same
reaction coordinate that I have used in SMD, I have tried to use the
distance component, choosing ligand atoms for group 1 and dummyAtom option
for group 2 (setting the appropriate coordinate to reproduce the same
reaction coordinate), but, still, it didn't work. I pasted the error message
below. Is it necessary to use another option together with dummyAtom?
Bests,Paulo
colvars:
----------------------------------------------------------------------
colvars: Initializing the collective variables module, version 29-09-2008.
colvars: # colvarsTrajFrequency = 500
colvars: # colvarsRestartFrequency = 500
colvars: # trajAppend = off [default]
colvars: The restart output state file will be "protabf-a.colvars.state".
colvars: The trajectory file will be "protabf-a.colvars.traj".
colvars: The final output state file will be "protabf-a.colvars.state".
colvars: # analysis = off [default]
colvars:
----------------------------------------------------------------------
colvars: Initializing a new collective variable.
colvars: # name = Distance
colvars: Initializing a new "distance" component.colvars: #
componentCoeff = 1 [default]
colvars: # componentExp = 1 [default]
colvars: # oneSiteSystemForce = off [default]
colvars: Initializing atom group "group1".
colvars: Atom group "group1" defined, 35 atoms, total mass = 650.977.
colvars: Initializing atom group "group2".
colvars: Atom group "group2" defined, 0 atoms, total mass =
1.colvars: All components initialized.
colvars: # width = 0.1
colvars: # lowerBoundary = 16
colvars: Lower boundary defined.
colvars: # upperBoundary = 31
colvars: Upper boundary defined.
colvars: # lowerWallConstant = 10
colvars: Applying a harmonic lower wall at 16, with coefficient 10.
colvars: # upperWallConstant = 10
colvars: Applying a harmonic upper wall at 31, with coefficient 10.
colvars: # extendedLagrangian = off [default]
colvars: # outputValue = on [default]
colvars: # outputVelocity = off [default]
colvars: # outputSystemForce = off [default]
colvars: # outputAppliedForce = off [default]
colvars: ------------------------------
----------------------------------------
colvars: Collective variables initialized, 1 in total.
colvars:
----------------------------------------------------------------------
colvars: Initializing a new "abf" instance.
colvars: # name = "abf1" [default]
colvars: # colvars = { Distance }
colvars: # applybias = on [default]
colvars: # hidejacobian = off [default]
colvars: Jacobian (geometric) forces will be included in reported free
energy gradients.
colvars: # fullsamples = 500
colvars: # inputprefix = [default]
colvars: # outputfreq = 500 [default]
colvars: Finished ABF setup.
colvars:
----------------------------------------------------------------------
colvars: Collective variables biases initialized, 1 in total.
colvars:
----------------------------------------------------------------------
colvars: Collective variables module initialized.
colvars:
----------------------------------------------------------------------
Info: Startup phase 7 took 0.012846 s, 7.72452 MB of memory in use
Info: Startup phase 8 took 0.000380039 s, 12.3929 MB of memory in use
Info: Finished startup at 0.541487 s, 12.3929 MB of memory in use
TCL: Running for 4000000 steps
ETITLE: TS BOND ANGLE DIHED
IMPRP ELECT VDW BOUNDARY
MISC KINETIC TOTAL TEMP
POTENTIAL TOTAL3 TEMPAVG PRESSURE
GPRESSURE VOLUME PRESSAVG GPRESSAVG
ENERGY: 0 849.8375 2408.4881 1348.5871
135.3159 -5237.1600 -1091.2560 0.0000
0.0000 3104.3467 1518.1595 292.6250 -1586.1873
1557.9272 292.6250 112.1152 111.0410
590148.0000 112.1152 111.0410
colvars: Error: system forces are not available from a dummy atom group.
colvars: If this error message is unclear, try recompile with
-DCOLVARS_DEBUG.
FATAL ERROR: Error in the collective variables module: exiting.
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Error in the collective variables module: exiting.
[0] Stack Traceback:
[0] CmiAbort+0x7f [0xa4526d]
[1] _Z8NAMD_diePKc+0x62 [0x500082]
[2] _ZN16colvarproxy_namd11fatal_errorERKSs+0x64 [0x844b68]
[3] _ZN12colvarmodule11fatal_errorERKSs+0x18 [0x79ae22]
[4] _ZNK12colvarmodule10atom_group12system_forceEv+0x53 [0x816f75]
[5] _ZN6colvar8distance19calc_force_invgradsEv+0xd7 [0x829145]
[6] _ZN6colvar4calcEv+0xc03 [0x7cca1f]
[7] _ZN12colvarmodule4calcEv+0x6c [0x7969bc]
[8] _ZN16colvarproxy_namd9calculateEv+0x497 [0x8415a1]
[9] _ZThn16_N16colvarproxy_namd9calculateEv+0xa [0x841108]
[10]
_ZN12GlobalMaster11processDataEPiS0_P6VectorS2_S2_S0_S0_S2_S0_S0_S2_+0x71
[0x77b165]
[11] _ZN18GlobalMasterServer11callClientsEv+0x469 [0x77f191]
[12] _ZN18GlobalMasterServer8recvDataEP20ComputeGlobalDataMsg+0x6f7
[0x77e7d7]
[13] _ZN10ComputeMgr21recvComputeGlobalDataEP20ComputeGlobalDataMsg+0x12
[0x569388]
[14]
_ZN18CkIndex_ComputeMgr48_call_recvComputeGlobalData_ComputeGlobalDataMsgEPvP10ComputeMgr+0xf
[0x569373]
[15] CkDeliverMessageFree+0x21 [0x9c2d71]
[16] _Z15_processHandlerPvP11CkCoreState+0x509 [0x9c2365]
[17] CsdScheduleForever+0xa5 [0xa4bcf5]
[18] CsdScheduler+0x1c [0xa4b8f6]
[19] _ZN7BackEnd7suspendEv+0xb [0x508add]
[20] _ZN9ScriptTcl7Tcl_runEPvP10Tcl_InterpiPPc+0x140 [0x8fcde4]
[21] TclInvokeStringCommand+0x91 [0xa6e208]
[22] namd2 [0xaa4058]
[23] Tcl_EvalEx+0x176 [0xaa469b]
[24] Tcl_EvalFile+0x134 [0xa9c0a4]
[25] _ZN9ScriptTcl3runEPc+0x14 [0x8fc4e2]
[26] _Z18after_backend_initiPPc+0x22b [0x50481b]
[27] main+0x3a [0x5045ba]
[28] __libc_start_main+0xe6 [0x7ff4b89e8466]
[29] _ZNSt8ios_base4InitD1Ev+0x52 [0x4ff9ea]
Charm++ fatal error:
FATAL ERROR: Error in the collective variables module: exiting.
Aborted
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