Re: vmd-l: namd CG minimization error: unable to find angle parameters for nxg nxx nxg

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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