Re: colvars: free energy change with rmsd

From: Kyle Hong (kforjob_at_gmail.com)
Date: Wed Apr 14 2010 - 04:05:03 CDT

*rom:* Dhiraj Srivastava (/dhirajks_at_gmail.com/
<mailto:dhirajks_at_gmail.com?Subject=Re:%20%20line%20too%20long%20in%20pdb%20file%20restart.coor>)
*Date:* Wed Oct 11 2006 - 18:12:54 CDT ??:
> should i use dcd file to write pdb for last frame or restart.coor
> file. i am
> not able to write pdb from restart.coor file.

Actually,I get the same problem with you ,I save the restart.coor as
restart.pdb and nothing write to
the pdb file (the file size is 0),can any one have some idea that fix
the line too long problem

with the restar.coor file ? Any sugguestion is very appreciate.

ps:follow is the confige file and the error message

*confige file*
structure grama.psf
coordinates nptsim_out.restart.coor
velocities nptsim_out.restart.vel
extendedSystem nptsim_out.restart.xsc
parameters par_all27_prot_lipid.inp
parameters par-extraterms.inp
paraTypeCharmm on

restartfreq 100000
outputEnergies 120
outputTiming 100
xstFreq 100
dcdFreq 100
wrapAll on
wrapNearest on

timestep 1
nonBondedFreq 2
fullElectFrequency 4
stepsPerCycle 20

switching on
switchDist 8.5
cutoff 10
pairlistdist 11.5
margin 2

Pme on
PmeGridsizeX 32
PmeGridsizeY 32
PmeGridsizeZ 64

exclude scaled1-4
1-4scaling 1.0

langevin on
langevinDamping 1
langevinTemp 310
langevinHydrogen no

langevinPiston on
langevinPistonTarget 1.01325
langevinPistonPeriod 200
langevinPistonDecay 500
langevinPistonTemp 310

useGroupPressure yes # smaller fluctuations
useFlexibleCell no # allow dimensions to fluctuate independently
useConstantRatio no # fix shape in x-y plane

binaryoutput off
outputname nptsim_out_continue3ns

firsttimestep 6709000
run 3291000 ;#3.2ns

*error message*
Info: TIME FOR READING PSF FILE: 0.0924048
FATAL ERROR: Line too long in pdbfile nptsim_out.restart.coor:
0 ??????^\ @?qG3<96>^T???<9b>k^K?t"???^S<80>^A?^X_at_S?Y<9f>O

------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Line too long in pdbfile nptsim_out.restart.coor:0
??????^\ @?qG3<96>^T???<9b>k^K?t"???^S<80>^A?^X_at_S?Y<9f>?? (^N]<?^T@@"

Info: 49 IMPROPER
Info: 0 CROSSTERM
Info: 89 VDW
Info: 0 VDW_PAIRS
Info: TIME FOR READING PSF FILE: 0.0924048
FATAL ERROR: Line too long in pdbfile nptsim_out.restart.coor:
0 ??????^\ @?qG3<96>^T???<9b>k^K?t"???^S<80>^A?^X_at_S?Y<9f>??
(^N]<?^T@@"?>7<86>????^[???$? ?<97><83>h<9f>?^[@<8c>?}P?r???5>?^Y_at_7??
?}<99>???\?z<89>?#?^???8:^\@^S??HD<89>??^C??QV^O% ?<97>^T
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Line too long in pdbfile nptsim_out.restart.coor:
0 ??????^\ @?qG3<96>^T???<9b>k^K?t"???^S<80>^A?^X_at_S?Y<9f>
Charm++ fatal error:
FATAL ERROR: Line too long in pdbfile nptsim_out.restart.coor:0 ??????^\
@?qG3<96>^T???<9b>k^K?t"???^S<80>^A?^X_at_S?Y<9f>?? (^N]<?^T@@"

  [0] Stack Traceback: [0] CmiAbort+0x7f [0xa26335] [1]
_Z8NAMD_diePKc+0x62 [0x507212] [2] _ZN3PDBC1EPKc+0x239 [0x8bba67]
[3] _ZN9NamdState14configListInitEP10ConfigList+0xe1a [0x883924] [4]
_ZN9ScriptTcl9initcheckEv+0x5e [0x8ee55c] [5]
_ZN9ScriptTcl7Tcl_runEPvP10Tcl_InterpiPPc+0x20 [0x8eae38] [6]
TclInvokeStringCommand+0x91 [0xa50808] [7] namd2 [0xa86658] [8]
Tcl_EvalEx+0x176 [0xa86c9b] [9] Tcl_EvalFile+0x134 [0xa7e6a4] [10]
_ZN9ScriptTcl3runEPc+0x14 [0x8ea656] [11]
_Z18after_backend_initiPPc+0x22b [0x50ba2b] [12] main+0x3a
[0x50b7ca] [13] __libc_start_main+0xf4 [0x3e9981d994]
   [14] _ZNSt8ios_base4InitD1Ev+0x72 [0x506b7a]
Type :quit<Enter> to exit Vim0x72 [0x506b7a]

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