error caused by atoms of lipid membrane

From: xiaojing gong (gongxiaojing1981_at_yahoo.com.cn)
Date: Mon Mar 20 2006 - 06:27:07 CST

Dear all,
         Thank you for your suggestions that had given to me.
         I use the VMD 1.8.3 to produce membrane -x 100, -y 100, but there is still error warnings in VMD. First I ignore these errors, and do minimization.BUT when I do the equilibrium, there is fatal error stopping the simulation. could anyone give some suggestions. The atoms in the error messages is all the atoms of lipid. The attachment is my conf file.
  TCL: Running for 300000 steps
ETITLE: TS BOND ANGLE DIHED IMP
          ELECT VDW BOUNDARY MISC KINET
          TOTAL TEMP TOTAL2 TOTAL3 TEMPA
       PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSA
  ENERGY: 0 718.7559 5519.2091 6735.0556 133.34
   -163453.7739 12453.0185 0.0000 0.0000 99999999.99
  99999999.9999 99999999.9999 99999999.9999 99999999.9999 99999999.99
  99999999.9999 99999999.9999 1040600.0000 99999999.9999 99999999.99
  ERROR: Margin is too small for 12 atoms during timestep 1.
ERROR: Incorrect nonbonded forces and energies may be calculated!
ERROR: Constraint failure in RATTLE algorithm for atom 2277!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Atom 11674 velocity is 4121.86 -4942.28 -8445.38 (limit is 10000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Atom 14 velocity is -112846 69886.3 -79773.3 (limit is 10000)
ERROR: Atoms moving too fast; simulation has become unstable.

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#forcefield
paratypecharmm on
parameters /home/user/siap/Gong_NAMD_2.6b1_Linux-amd64/min5000steps/par_all27_prot_lipid.inp
#molecules
structure /home/user/siap/Gong_NAMD_2.6b1_Linux-amd64/min5000steps/ions_added.psf
coordinates /home/user/siap/Gong_NAMD_2.6b1_Linux-amd64/min5000steps/ions_added.pdb
                                       
outputname /home/user/siap/Gong_NAMD_2.6b1_Linux-amd64/min5000steps/5000_min
restartfreq 50
DCDfile /home/user/siap/Gong_NAMD_2.6b1_Linux-amd64/min5000steps/5000_min.dcd
DCDfreq 50
binaryoutput yes
binaryrestart yes
outputEnergies 100
wrapAll on
wrapNearest on

temperature 310

#temp & pressure coupling
langevin on
langevinTemp 310
langevinDamping 1

                                                             
#integrator
timestep 1
nonbondedFreq 2
fullElectFrequency 4
stepspercycle 20
                                                             
#approximations
rigidBonds all
rigidTolerance 0.00000001
cutoff 12
switching on
switchdist 10
pairlistdist 15
margin 4.0
exclude scaled1-4
1-4scaling 1.0 # 1.0 for Charmm, 0.833333 for Amber
                                       
cellBasisVector1 110 0. 0.
cellBasisVector2 0. 110 0.
cellBasisVector3 0. 0. 86
cellOrigin 2.6 2.2 2.1

PME on
PMEProcessors 20
PMEGridSizeX 110
PMEGridSizeY 110
PMEGridSizeZ 90
                                                             
fixedAtoms on
fixedAtomsFile /home/user/siap/Gong_NAMD_2.6b1_Linux-amd64/min5000steps/fix_backbone.pdb
fixedAtomsCol B

#IMDon yes
#IMDport 3000 ;# port number (enter it in VMD)
#IMDfreq 1 ;# send every 1 frame
#IMDwait on ;# wait for VMD to connect before running?

#minimization on
#minTinyStep 1.0e-6
#minBabyStep 1.0e-2
#minLineGoal 1.0e-4

minimize 5000
                                                             
                                                             


#forcefield
paratypecharmm on
parameters /home/user/siap/Gong_NAMD_2.6b1_Linux-amd64/300ps_fixrun/par_all27_prot_lipid.inp
                                                                 
#molecules
structure /home/user/siap/Gong_NAMD_2.6b1_Linux-amd64/300ps_fixrun/ions_added.psf
coordinates /home/user/siap/Gong_NAMD_2.6b1_Linux-amd64/300ps_fixrun/ions_added.pdb
bincoordinates /home/user/siap/Gong_NAMD_2.6b1_Linux-amd64/300ps_fixrun/5000_min.coor
binvelocities /home/user/siap/Gong_NAMD_2.6b1_Linux-amd64/300ps_fixrun/5000_min.vel
#extendedSystem /home/user/siap/Gong_NAMD_2.6b1_Linux-amd64/300ps_fixrun/5000_min.xsc

cellBasisVector1 110 0. 0.
cellBasisVector2 0. 110 0.
cellBasisVector3 0. 0. 86
cellOrigin 2.6 2.2 2.1

#temperature 310
#temp & pressure coupling
langevin on
langevinTemp 310
langevinDamping 1

useGroupPressure yes
useFlexibleCell no
LangevinPiston on
LangevinPistonTarget 1.01325
LangevinPistonPeriod 200
LangevinPistonDecay 500
LangevinPistonTemp 300
                                                                 
#output
outputname /home/user/siap/Gong_NAMD_2.6b1_Linux-amd64/300ps_fixrun/300ps_sim
outputEnergies 50
restartfreq 100
DCDfreq 100
DCDfile /home/user/siap/Gong_NAMD_2.6b1_Linux-amd64/300ps_fixrun/300ps_sim.dcd
binaryoutput yes
binaryrestart yes
                                      
wrapAll on
wrapNearest on
                                                             
#integrator
timestep 1
nonbondedFreq 2
fullElectFrequency 4
stepspercycle 20
                                                             
#approximations
rigidBonds all
rigidTolerance 0.00000001
cutoff 12
switching on
switchdist 10
pairlistdist 15
margin 4.0
exclude scaled1-4
1-4scaling 1.0 # 1.0 for Charmm, 0.833333 for Amber
                                       

PME on
PMEProcessors 16
PMEGridSizeX 110
PMEGridSizeY 110
PMEGridSizeZ 90
                                                             
fixedAtoms on
fixedAtomsFile /home/user/siap/Gong_NAMD_2.6b1_Linux-amd64/300ps_fixrun/fix_backbone.pdb
fixedAtomsCol B

run 300000
                                                             
                                                             

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