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bay__gulf金虫 (著名写手)
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104楼2009-11-15 13:28:39
NAMD 出错请求帮助！！
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小木虫(金币+0.5):给个红包，谢谢回帖交流
小木虫(金币+0.5):给个红包，谢谢回帖交流
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------------- Processor 0 Exiting: Called CmiAbort ------------ Reason: FATAL ERROR: can't read "coorList(577)": no such element in array while executing "lindex $coorList($i) 2" (procedure "calcforces" line 5) invoked from within "calcforces" Charm++ fatal error: FATAL ERROR: can't read "coorList(577)": no such element in array while executing "lindex $coorList($i) 2" (procedure "calcforces" line 5) invoked from within "calcforces" This application has requested the Runtime to terminate it in an unusual way. Please contact the application's support team for more information. 请问怎么解决这一问题？？ |
106楼2009-11-16 16:49:11
上面问题的.conf文件
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小木虫(金币+0.5):给个红包，谢谢回帖交流
小木虫(金币+0.5):给个红包，谢谢回帖交流
|
############################################################# ## JOB DESCRIPTION ## ############################################################# # Simulate the 4-nanotube system with induced pressure difference ############################################################# ## ADJUSTABLE PARAMETERS ## ############################################################# structure cnt.psf coordinates cnt.pdb set temperature 300 set outputname sim_short # Continuing a job from the restart files Bincoordinates initial.coor Binvelocities initial.vel ############################################################# ## SIMULATION PARAMETERS ## ############################################################# # Input paraTypeCharmm on parameters par_all27_prot_lipid.prm # Periodic Boundary conditions cellBasisVector1 23 0. 0. cellBasisVector2 0. 19.919 0. cellBasisVector3 0. 0 30.3962 wrapAll on # Force-Field Parameters exclude scaled1-4 1-4scaling 1.0 cutoff 12. switching on switchdist 10. pairlistdist 14.5 # Integrator Parameters timestep 1 ;# 1fs/step nonbondedFreq 2 fullElectFrequency 4 stepspercycle 20 # Constant Temperature Control langevin on ;# do langevin dynamics langevinDamping 5 ;# damping coefficient (gamma) of 5/ps langevinTemp $temperature langevinHydrogen no ;# don't couple langevin bath to hydrogens # Output outputName $outputname restartfreq 1000 ;# 1000steps = every 1ps dcdfreq 1000 outputEnergies 1000 # Fixed Atoms Constraint (set PDB occupancy-column to 1) fixedAtoms on # IMD Settings (can view sim in VMD) if {0} { IMDon on IMDport 3000 ;# port number (enter it in VMD) IMDfreq 1 ;# send every 1 frame IMDwait no ;# wait for VMD to connect before running? } ############################################################# ## EXTRA PARAMETERS ## ############################################################# tclForces on tclForcesScript { set cellLengthZ 30.3962 ;# The length of the unit cell in the z-direction, should be the same as the value in "cellBasisVector3" set LowerBoundary -12.5 set UpperBoundary 12.5 set force {0 0 0.4} set watIdList {} for {set i 577} {$i<1320} {incr i 3} { lappend watIdList $i addatom $i } proc calcforces {} { global cellLengthZ LowerBoundary UpperBoundary force watIdList loadcoords coorList foreach i $watIdList { set z [lindex $coorList($i) 2] set z [expr $z-round($z/$cellLengthZ)*$cellLengthZ] ;# Translate this coordinate into its corresponding value in the original unit cell if {$z>$UpperBoundary || $z<$LowerBoundary} { addforce $i $force } } } } ############################################################# ## EXECUTION SCRIPT ## ############################################################# run 40000 ;# 40ps |
107楼2009-11-16 17:03:39
上面问题的.conf文件
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小木虫(金币+0.5):给个红包，谢谢回帖交流
小木虫(金币+0.5):给个红包，谢谢回帖交流
|
############################################################# ## JOB DESCRIPTION ## ############################################################# # Simulate the 4-nanotube system with induced pressure difference ############################################################# ## ADJUSTABLE PARAMETERS ## ############################################################# structure cnt.psf coordinates cnt.pdb set temperature 300 set outputname sim_short # Continuing a job from the restart files Bincoordinates initial.coor Binvelocities initial.vel ############################################################# ## SIMULATION PARAMETERS ## ############################################################# # Input paraTypeCharmm on parameters par_all27_prot_lipid.prm # Periodic Boundary conditions cellBasisVector1 23 0. 0. cellBasisVector2 0. 19.919 0. cellBasisVector3 0. 0 30.3962 wrapAll on # Force-Field Parameters exclude scaled1-4 1-4scaling 1.0 cutoff 12. switching on switchdist 10. pairlistdist 14.5 # Integrator Parameters timestep 1 ;# 1fs/step nonbondedFreq 2 fullElectFrequency 4 stepspercycle 20 # Constant Temperature Control langevin on ;# do langevin dynamics langevinDamping 5 ;# damping coefficient (gamma) of 5/ps langevinTemp $temperature langevinHydrogen no ;# don't couple langevin bath to hydrogens # Output outputName $outputname restartfreq 1000 ;# 1000steps = every 1ps dcdfreq 1000 outputEnergies 1000 # Fixed Atoms Constraint (set PDB occupancy-column to 1) fixedAtoms on # IMD Settings (can view sim in VMD) if {0} { IMDon on IMDport 3000 ;# port number (enter it in VMD) IMDfreq 1 ;# send every 1 frame IMDwait no ;# wait for VMD to connect before running? } ############################################################# ## EXTRA PARAMETERS ## ############################################################# tclForces on tclForcesScript { set cellLengthZ 30.3962 ;# The length of the unit cell in the z-direction, should be the same as the value in "cellBasisVector3" set LowerBoundary -12.5 set UpperBoundary 12.5 set force {0 0 0.4} set watIdList {} for {set i 577} {$i<1320} {incr i 3} { lappend watIdList $i addatom $i } proc calcforces {} { global cellLengthZ LowerBoundary UpperBoundary force watIdList loadcoords coorList foreach i $watIdList { set z [lindex $coorList($i) 2] set z [expr $z-round($z/$cellLengthZ)*$cellLengthZ] ;# Translate this coordinate into its corresponding value in the original unit cell if {$z>$UpperBoundary || $z<$LowerBoundary} { addforce $i $force } } } } ############################################################# ## EXECUTION SCRIPT ## ############################################################# run 40000 ;# 40ps |
109楼2009-11-16 18:11:47
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小木虫(金币+0.5):给个红包，谢谢回帖交流
小木虫(金币+0.5):给个红包，谢谢回帖交流
|
我的问题运行.conf时，提示： ------------- Processor 0 Exiting: Called CmiAbort ------------ Reason: FATAL ERROR: can't read "coorList(577)": no such element in array while executing "lindex $coorList($i) 2" (procedure "calcforces" line 5) invoked from within "calcforces" Charm++ fatal error: FATAL ERROR: can't read "coorList(577)": no such element in array while executing "lindex $coorList($i) 2" (procedure "calcforces" line 5) invoked from within "calcforces" This application has requested the Runtime to terminate it in an unusual way. Please contact the application's support team for more information. 怎样才能解决啊？ |
111楼2009-11-18 16:36:27
113楼2009-11-24 10:37:17