From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Fri Dec 11 2009 - 09:52:43 CST
On Fri, Dec 11, 2009 at 2:07 AM, Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
> Please keep the relevant mailing list copied on such discussions.
>
> You shouldn't use rigidbonds in rbcg simulations -- it only applies to
> hydrogen atoms, and there aren't any in rbcg simulations.
>
> There does appear to be a missing line in the parameter file; we've
> never run across it because we've never done simulations with two
> glycines one residue apart before. Please try adding
> Nxg Nxx Nxg 2.988 92
> to the ANGLES section of the parameter file and see if that helps.
Hello Peter:
That done what you suggested the procedure started
>From log file:
.................
Info: 1 NAMD 2.7b1 Linux-x86_64 4 tya64 francesco
Info: Running on 4 processors.
Info: Charm++/Converse parallel runtime startup completed at 0.00522494 s
Info: 1.63356 MB of memory in use based on CmiMemoryUsage
Info: Configuration file is minimize.conf
TCL: Suspending until startup complete.
Info: SIMULATION PARAMETERS:
.....................
MINIMIZER SLOWLY MOVING ATOMS WITH BAD CONTACTS DOWNHILL
LINE MINIMIZER REDUCING GRADIENT
LINE MINIMIZER BRACKET
MINIMIZER RESTARTING CONJUGATE GRADIENT ALGORITHM
START OF LOAD BALANCING
END OF LOAD BALANCING
and in between
PRESSURE
GPRESSURE
ENERGY
All that was written immediately or so. I am now back to the computer
after about 7 hours, nothing more has been written to the log file,
which ends
PRESSURE: 536 4.3726e+07 -3.65201e+06 -603130 -1.20214e+06 5.36183e+07
1.62009e+06 -1.70818e+06 9.75261e+06 4.96014e+07
GPRESSURE: 536 4.3726e+07 -3.65201e+06 -603130 -1.20214e+06
5.36183e+07 1.62009e+06 -1.70818e+06 9.75261e+06 4.96014e+07
ENERGY: 536 1474.2549 6309.1780 11699.6826
0.0000 -2455.1826 187157485.0132 0.0000
0.0000 0.0000 187174512.9461 0.0000
187174512.9461 187174512.9461 0.0000 48981892.1629
48981892.1629 1178217.0000 48981892.1629 48981892.1629
The only other files written are
.xst
.xst.BAK
FFTW_NAMD_2.7b1_Linux-x86_64.txt
Command top show a single PID for namd2 with 100% cpu.
I can only kill the process and think about.
francesco
Top command shows just one PID for namd2 with 100%cpu
Then I killed
> Best,
> Peter
>
> Francesco Pietra wrote:
>> Hello Peter
>>
>> On Thu, Dec 10, 2009 at 10:06 PM, Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
>>
>>> Hi Francesco,
>>> did you directly copy/paste that error message? There shouldn't be any
>>> beads named nxx or nxg, only Nxx and Nxg.
>>>
>>
>> Yes, capital N
>>
>>> Also, you should always use "exclude 1-2" in rbcg simulations. There's
>>> no such thing as scaled1-2, and the force field was not designed for use
>>> with 1-4 exclusions.
>>>
>>
>> I had adapted the conf files from the membrane tutorial for all-atoms.
>> Now, with "exclude 1-2", the error is:
>>
>> Charm++ fatal error:
>> FATAL ERROR: splitPatch hydrogen is required for rigidBonds
>>
>>
>> Perhaps, it would be quicker by having a look at the conf file I am
>> using to minimize if there is any other major mistake:
>>
>> #############################################################
>> ## JOB DESCRIPTION ##
>> #############################################################
>>
>> # Min. and Eq. of mod21.min
>> # embedded in POPC membrane and water solvated (no ions added).
>> # Protein and POPC constrained. PME, Constant Volume
>>
>> #############################################################
>> ## ADJUSTABLE PARAMETERS ##
>> #############################################################
>>
>> structure /workingdir/popc.128_mod21_W.psf
>> coordinates /workingdir/popc.128_mod21_W.pdb
>> outputName popc_mod21_W_min
>>
>> set temperature 300
>>
>> # Continuing a job from the restart files
>> if {0} {
>> set inputname popc_mod21_W
>> binCoordinates $inputname.restart.coor
>> binVelocities $inputname.restart.vel ;# remove the "temperature"
>> entry if you use this!
>> extendedSystem $inputname.restart.xsc
>> }
>>
>> firsttimestep 0
>>
>>
>> #############################################################
>> ## SIMULATION PARAMETERS ##
>> #############################################################
>>
>> # Input
>> paraTypeCharmm on
>> parameters /workingdir/rbcg-2007.par
>>
>> # NOTE: Do not set the initial velocity temperature if you
>> # have also specified a .vel restart file!
>> temperature $temperature
>>
>>
>> # Periodic Boundary Conditions
>> # NOTE: Do not set the periodic cell basis if you have also
>> # specified an .xsc restart file!
>> if {1} {
>> cellBasisVector1 103. 0. 0.
>> cellBasisVector2 0. 123. 0.
>> cellBasisVector3 0. 0. 93.
>> cellOrigin 42.90500259399414 44.24656295776367 30.877103805541992
>> }
>> wrapWater on
>> wrapAll on
>>
>>
>> # Force-Field Parameters
>> exclude 1-2
>> cutoff 12.
>> switching on
>> switchdist 10.
>> pairlistdist 13.5
>>
>>
>> # Integrator Parameters
>> timestep 10.0 ;# 10fs/step
>> rigidBonds all ;# needed for 2fs steps
>> nonbondedFreq 1
>> fullElectFrequency 2
>> stepspercycle 20
>>
>>
>> #PME (for full-system periodic electrostatics)
>> if {1} {
>> PME yes
>> PMEGridSizeX 103
>> PMEGridSizeY 123
>> PMEGridSizeZ 93
>> }
>>
>>
>> # Constant Temperature Control
>> langevin on ;# do langevin dynamics
>> langevinDamping 1 ;# damping coefficient (gamma) of 5/ps
>> langevinTemp $temperature
>>
>> # Constant Pressure Control (variable volume)
>> if {0} {
>> useGroupPressure yes ;# needed for 2fs steps
>> useFlexibleCell yes ;# no for water box, yes for membrane
>> useConstantArea no ;# no for water box, yes for membrane
>>
>> langevinPiston on
>> langevinPistonTarget 1.01325 ;# in bar -> 1 atm
>> langevinPistonPeriod 200.
>> langevinPistonDecay 50.
>> langevinPistonTemp $temperature
>> }
>>
>>
>> restartfreq 1000 ;# 1000steps = every 2ps
>> dcdfreq 1000
>> xstFreq 1000
>> outputEnergies 50
>> outputPressure 50
>>
>>
>> # Fixed Atoms Constraint (set PDB beta-column to 1)
>> if {1} {
>> fixedAtoms on
>> fixedAtomsFile popc.128_mod21_W.fix
>> fixedAtomsCol B
>> fixedAtomsForces on
>> }
>>
>> #############################################################
>> ## EXTRA PARAMETERS ##
>> #############################################################
>>
>> # Put here any custom parameters that are specific to
>> # this job (e.g., SMD, TclForces, etc...)
>>
>> # constraints on
>> # consexp 2
>> # consref popc.128_mod21_W.pdb
>> # conskfile kcsa_popcwi.cnst
>> # conskcol B
>> # margin 3
>>
>> # tclforces on
>> # set waterCheckFreq 100
>> # set lipidCheckFreq 100
>> # set allatompdb ../02-MEMBRANE/kcsa_popcwi.pdb
>> # tclForcesScript keep_water_out.tcl
>>
>> # eFieldOn yes
>> # eField 0 0 -0.155
>>
>>
>> #############################################################
>> ## EXECUTION SCRIPT ##
>> #############################################################
>>
>> # Minimization
>> if {1} {
>> minimize 2000
>> reinitvels $temperature
>> }
>>
>> run 50000 ;# 0.5 ns
>> ===============
>>
>> Thanks
>> francesco
>>
>>
>>
>>
>>
>>> Best,
>>> Peter
>>>
>>> Francesco Pietra wrote:
>>>
>>>> I am trying to minimize at const vol a CG system
>>>> protein-popcbilayer-water with protein and bilayer restrained. After
>>>> adjusting the conf file on the basis of errors messages, I am getting
>>>> an error "unable to find angle parameters for nxg nxx nxg" which I
>>>> could not remedy although I have followed the thread with same error.
>>>>
>>>> The conf file
>>>>
>>>> # Input
>>>> paraTypeCharmm on
>>>> parameters /workingdir/rbcg-2007.par
>>>>
>>>> means that the par file is in the working dir and it contains the
>>>> requested parameters. Is rbcg-2007.par not enough? In particular, how
>>>> to give parameters for the POPC lipid, which are not comprised in that
>>>> par file?
>>>>
>>>> But I was suspicious that the above setting of parameters is incorrect
>>>> because if I modify
>>>>
>>>> # Force-Field Parameters
>>>> exclude scaled1-4
>>>> 1-4scaling 1.0
>>>> cutoff 12.
>>>> switching on
>>>> switchdist 10.
>>>> pairlistdist 13.5
>>>>
>>>> to scaling 1-2 (as I have seen in a thread for CG), I get "Error: 1-2
>>>> scaling". Which seems to me to imply that the procedure is assuming -
>>>> from the above input -an all-atoms system.
>>>>
>>>> Thanks for help
>>>>
>>>> francesco pietra
>>>>
>>>>
>>>
>
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