From: Yoav Beck (ucbpybe_at_ucl.ac.uk)
Date: Thu Aug 06 2009 - 07:46:05 CDT
Dear Narender,
Thanks for your tip. Unfortunately, I am now running in different
errors. I ran minimization with the protein and membrane constrained,
but cannot conclude successfully.
As before, minimization start with huge numbers
TCL: Minimizing for 5000 steps
PRESSURE: 0 6.53273e+16 4.60271e+16 -2.23605e+17 3.96669e+16 2.88557e+16
1.74669e+17 -2.52879e+16 -3.79973e+15 1.19747e+16
GPRESSURE: 0 6.53273e+16 4.60271e+16 -2.23605e+17 3.96669e+16
2.88557e+16 1.74669e+17 -2.52879e+16 -3.79973e+15 1.19747e+16
ETITLE: TS BOND ANGLE DIHED
IMPRP ELECT VDW BOUNDARY
MISC KINETIC TOTAL TEMP
POTENTIAL TOTAL3 TEMPAVG PRESSURE
GPRESSURE VOLUME PRESSAVG GPRESSAVG
ENERGY: 0 2218.5741 540.2636 0.0000
0.0000 -202489.5481 9999999999.9999 0.0000
0.0000 0.0000 9999999999.9999 0.0000
9999999999.9999 9999999999.9999 0.0000 9999999999.9999
9999999999.9999 102600.0000 9999999999.9999 9999999999.9999
..
MINIMIZER SLOWLY MOVING ATOMS WITH BAD CONTACTS DOWNHILL
TIMING: 5000 CPU: 2167.31, 0.438185/step Wall: 3596.54, 0.708983/step,
0 hours remaining, 134.361786 MB of memory in use.
PRESSURE: 5000 1.24909e+09 -1.62579e+08 -3.763e+08 2.92839e+07
1.71229e+09 -2.63983e+07 -1.25611e+07 5.63724e+06 1.68225e+09
GPRESSURE: 5000 1.27878e+09 -1.63836e+08 -3.78217e+08 2.42504e+07
1.73824e+09 -2.81582e+07 -1.22454e+07 3.88684e+06 1.70974e+09
ETITLE: TS BOND ANGLE DIHED
IMPRP ELECT VDW BOUNDARY
MISC KINETIC TOTAL TEMP
POTENTIAL TOTAL3 TEMPAVG PRESSURE
GPRESSURE VOLUME PRESSAVG GPRESSAVG
ENERGY: 5000 777782.6964 72735.3453 0.0000
0.0000 -158525.6328 568191931.6427 0.0000
0.0000 0.0000 568883924.0516 0.0000 568883924.0516
568883924.0516 0.0000 1547874704.4990 1575585906.7949
102600.0000 1547874704.4990 1575585906.7949
WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 5000
REINITIALIZING VELOCITIES AT STEP 5000 TO 310 KELVIN.
TCL: Running for 5000 steps
PRESSURE: 5000 nan nan nan nan nan nan nan nan nan
GPRESSURE: 5000 nan nan nan nan nan nan nan nan nan
ETITLE: TS BOND ANGLE DIHED
IMPRP ELECT VDW BOUNDARY
MISC KINETIC TOTAL TEMP
POTENTIAL TOTAL3 TEMPAVG PRESSURE
GPRESSURE VOLUME PRESSAVG GPRESSAVG
ENERGY: 5000 0.0000 0.0000 0.0000
0.0000 -198689.6497 9999999999.9999 0.0000 0.0000
9999999999.9999 9999999999.9999 9999999999.9999 9999999999.9999
9999999999.9999 9999999999.9999 9999999999.9999 9999999999.9999
102600.0000 9999999999.9999 9999999999.9999
ERROR: Margin is too small for 26958 atoms during timestep 5001.
ERROR: Incorrect nonbonded forces and energies may be calculated!
FATAL ERROR: Periodic cell has become too small for original patch grid!
Possible solutions are to restart from a recent checkpoint,
increase margin, or disable useFlexibleCell for liquid simulation.
------------- Processor 12 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Periodic cell has become too small for original
patch grid!
Possible solutions are to restart from a recent checkpoint,
increase margin, or disable useFlexibleCell for liquid simulation.
FATAL ERROR: Periodic cell has become too small for original patch grid!
Possible solutions are to restart from a recent checkpoint,
increase margin, or disable useFlexibleCell for liquid simulation.
------------- Processor 14 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Periodic cell has become too small for original
patch grid!
Possible solutions are to restart from a recent checkpoint,
increase margin, or disable useFlexibleCell for liquid simulation.
FATAL ERROR: Periodic cell has become too small for original patch grid!
Possible solutions are to restart from a recent checkpoint,
increase margin, or disable useFlexibleCell for liquid simulation.
------------- Processor 1 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Periodic cell has become too small for original
patch grid!
Possible solutions are to restart from a recent checkpoint,
increase margin, or disable useFlexibleCell for liquid simulation.
FATAL ERROR: Periodic cell has become too small for original patch grid!
Possible solutions are to restart from a recent checkpoint,
increase margin, or disable useFlexibleCell for liquid simulation.
------------- Processor 2 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Periodic cell has become too small for original
patch grid!
Possible solutions are to restart from a recent checkpoint,
increase margin, or disable useFlexibleCell for liquid simulation.
[2] Stack Traceback:
[0] CmiAbort+0x5f [0xa4b62f]
[1] _Z8NAMD_diePKc+0x62 [0x4ffe02]
[2] _ZN9HomePatch13doMarginCheckEv+0x235 [0x85cfab]
[3] _ZN9HomePatch14positionsReadyEi+0x63 [0x85bd29]
[4] _ZN9Sequencer17runComputeObjectsEii+0xad [0x907f71]
[5] _ZN9Sequencer9integrateEv+0x1186 [0x904ad0]
[6] _ZN9Sequencer9algorithmEv+0x32e [0x9015fe]
FATAL ERROR: Periodic cell has become too small for original patch grid!
Possible solutions are to restart from a recent checkpoint,
increase margin, or disable useFlexibleCell for liquid simulation.
------------- Processor 10 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Periodic cell has become too small for original
patch grid!
Possible solutions are to restart from a recent checkpoint,
increase margin, or disable useFlexibleCell for liquid simulation.
FATAL ERROR: Periodic cell has become too small for original patch grid!
Possible solutions are to restart from a recent checkpoint,
increase margin, or disable useFlexibleCell for liquid simulation.
.. Then sane message for each processor.
[1] Stack Traceback:
[0] CmiAbort+0x5f [0xa4b62f]
[1] _Z8NAMD_diePKc+0x62 [0x4ffe02]
[2] _ZN9HomePatch13doMarginCheckEv+0x235 [0x85cfab]
[3] _ZN9HomePatch14positionsReadyEi+0x63 [0x85bd29]
[4] _ZN9Sequencer17runComputeObjectsEii+0xad [0x907f71]
[5] _ZN9Sequencer9integrateEv+0x1186 [0x904ad0]
[6] _ZN9Sequencer9algorithmEv+0x32e [0x9015fe]
[7] _ZN9Sequencer9threadRunEPS_+0xe [0x90e982]
[8] CthStartThread+0x20 [0x9b6d72]
[7] _ZN9Sequencer9threadRunEPS_+0xe [0x90e982]
[8] CthStartThread+0x20 [0x9b6d72]
[9] /lib64/tls/libc.so.6 [0x3247c3e7f0]
Fatal error on PE 2> FATAL ERROR: Periodic cell has become too small for
original patch grid!
Possible solutions are to restart from a recent checkpoint,
increase margin, or disable useFlexibleCell for liquid simulation.
The script is as follow:
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 10.
pairlistdist 13.5
timestep 2.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10
langevin on ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen off ;# don't couple langevin bath to hydrogens
cellBasisVector1 50 0. 0.
cellBasisVector2 0. 27 0.
cellBasisVector3 0. 0 76
cellOrigin .32 .57 -.19
wrapAll on
PME yes
PMEGridSizeX 81
PMEGridSizeY 45
PMEGridSizeZ 128
useGroupPressure yes ;# needed for rigidBonds
useFlexibleCell yes
useConstantArea yes
langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.
langevinPistonDecay 50.
langevinPistonTemp $temperature.
restartfreq 500 ;# 500steps = every 1ps
dcdfreq 100
xstFreq 250
outputEnergies 100
outputPressure 100
if {1} {
fixedAtoms on
fixedAtomsFile papc_wat.ref
fixedAtomsCol B
}
I have tried differents PME grid size (here is the largest I tried). I
also ran simulation with flexiblecell and constantarea turned off. The
outcome was exactly the same. I am about to restart the simulation with
water molecule further away from the protein (solvate with a larger cut
off). Other than that I am pretty much stuck. So again any help will be
very appreciate.
Thanks.
Yoav.
Narender Singh Maan wrote:
> I think its better to go step by step.
> 1)EM just the waters (everything else restrained)
> 2) EM water and lipid (protein restrained)
> 3) EM all
> 4) than its better to do small MD for lipid (membrane) alone keeping
> protein restrained. See if it stabalize....
> 5) MD all
> .................
> also i dont think keeping 100000 steps EM is good.......start with
> ~5000 and see your gradient and proceed accordingly....
> -NS
>
> On Tue, Aug 4, 2009 at 11:08 AM, Yoav Beck <ucbpybe_at_ucl.ac.uk
> <mailto:ucbpybe_at_ucl.ac.uk>> wrote:
>
> Dear all,
> I am trying to run membrane protein simulations, but can't
> minimize successfully. I did combine the protein with the
> membrane, add water and counter ions. Here is an extract of the
> outcome
>
> PRESSURE: 0 9.46948e+15 -1.39942e+14 1.54387e+14 -1.39942e+14
> 1.11476e+16 -2.23902e+14 1.54387e+14 -2.23902e+14 1.02628e+16
> GPRESSURE: 0 9.46948e+15 -1.39942e+14 1.54387e+14 -1.39942e+14
> 1.11476e+16 -2.23902e+14 1.54387e+14 -2.23902e+14 1.02628e+16
> ETITLE: TS BOND ANGLE DIHED
> IMPRP ELECT VDW BOUNDARY
> MISC KINETIC TOTAL TEMP
> POTENTIAL TOTAL3 TEMPAVG PRESSURE
> GPRESSURE VOLUME PRESSAVG GPRESSAVG
>
> ENERGY: 0 6937.4145 8879.2601 8448.2516
> 68.9126 -2395.3259 9999999999.9999 0.0000
> 0.0000 0.0000 9999999999.9999 0.0000
> 9999999999.9999 9999999999.9999 0.0000
> 9999999999.9999 9999999999.9999 102300.0000 9999999999.9999
> 9999999999.9999
>
> OPENING EXTENDED SYSTEM TRAJECTORY FILE
> MINIMIZER SLOWLY MOVING ATOMS WITH BAD CONTACTS DOWNHILL
> PRESSURE: 1 6.02846e+14 4.11297e+12 -2.47166e+14 4.11297e+12
> 5.42603e+14 -5.55522e+13 -2.47166e+14 -5.55522e+13 5.3318e+14
> GPRESSURE: 1 6.02846e+14 4.11296e+12 -2.47166e+14 4.11298e+12
> 5.42602e+14 -5.55522e+13 -2.47166e+14 -5.55521e+13 5.3318e+14
> ENERGY: 1 150887.6550 46650.6159 9886.1746
> 961.3403 -11626.6565 9999999999.9999 0.0000
> 0.0000 0.0000 9999999999.9999 0.0000
> 9999999999.9999 9999999999.9999 0.0000
> 9999999999.9999 9999999999.9999 102300.0000 9999999999.9999
> 9999999999.9999
> ..
> MINIMIZER SLOWLY MOVING ATOMS WITH BAD CONTACTS DOWNHILL
> PRESSURE: 97414 3.37775e+09 1.09931e+07 -2.91043e+06 1.09931e+07
> 3.40785e+09 -4.73679e+06 -2.91043e+06 -4.73679e+06 3.33555e+09
> GPRESSURE: 97414 3.46918e+09 1.42519e+07 -3.95821e+06 1.4462e+07
> 3.44516e+09 -5.05362e+06 8.23537e+06 -6.33855e+06 3.44226e+09
> ENERGY: 97414 4874838.3038 937325.7014 31077.7472
> 38194.6180 -69456.1542 1238003572.7904 0.0000
> 0.0000 0.0000 1243815553.0065 0.0000
> 1243815553.0065 1243815553.0065 0.0000
> 3373713815.5463 3452199270.2683 102300.0000 3373713815.5463
> 3452199270.2683
> The high vdw number is probably due to clashes between atoms, but
> the PRESSURE and GPRESSURE lines are ununderstandable to me. The
> script looks like
>
> set temperature 310
> firsttimestep 0
>
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 12.
> switching on
> switchdist 10.
> pairlistdist 13.5
>
> timestep 2.0 ;# 2fs/step
> rigidBonds all ;# needed for 2fs steps
> nonbondedFreq 1
> fullElectFrequency 2 stepspercycle 10
>
> langevin on ;# do langevin dynamics
> langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
> langevinTemp $temperature
> langevinHydrogen off ;# don't couple langevin bath to hydrogens
>
> cellBasisVector1 66 0. 0.
> cellBasisVector2 0. 31 0.
> cellBasisVector3 0. 0. 50
> cellOrigin 0. 0. 0.
> wrapAll on
> PME yes
> PMEGridSizeX 72
> PMEGridSizeY 32
> PMEGridSizeZ 64
>
> useGroupPressure yes ;# needed for rigidBonds
> useFlexibleCell yes
> useConstantArea yes
>
> langevinPiston on
> langevinPistonTarget 1.01325 ;# in bar -> 1 atm
> langevinPistonPeriod 100.
> langevinPistonDecay 50.
> langevinPistonTemp $temperature
>
> restartfreq 500 ;# 500steps = every 1ps
> dcdfreq 100
> xstFreq 250
> outputEnergies 100
> outputPressure 100
>
> minimize 100000
> reinitvels $temperature
>
> Any help will be greatly appreciate.
>
> Cheers,
>
> Yoav.
>
>
>
>
>
>
>
>
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:53:08 CST