Re: PROTEIN VACUUM MINIMIZATION ERROR

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Sat May 24 2008 - 20:46:34 CDT

Hi Samuel,
what happens to the hydrogen atom during the trajectory that you look
at? Have you tried writing a dcd at every timestep to see if you can
observe its motion becoming unstable? Is it, for example, clashing with
a fixed atom? What is the rms gradient at the end of your minimization?
Peter

Semorale wrote:
> Hello NAMD users!
>
> I want to make a vacuum minimization for a protein of 15000 atoms,
> with fix protein backbone. I tried several configurations, but in all
> appears this error for the same hydrogen atom:
>
> WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 11000
> ERROR: Atom 5211 velocity is 32723.6 20404.1 21559.3 (limit is 12000)
> ERROR: Atoms moving too fast; simulation has become unstable.
> ERROR: Exiting prematurely.
>
>
> I have reviewed the DCD and apparently did not see anything strange
> ... *how could solve this?*
> *Reply please!!*
> Thanks you very much for yours great help!!
>
> SAMUEL.
>
> *my last configuration:*
>
> # Input
> paraTypeCharmm on
> parameters par_all27_prot_lipid.prm
> #parameters par-extraterms.inp
> temperature $temperature
>
> # Force-Field Parameters
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 12
> switching on
> switchdist 10
> pairlistdist 14
>
> # Integrator Parameters
> timestep 1.0 ;# 1fs/step (2)
> rigidBonds none ;# needed for 1fs steps (2)
> nonbondedFreq 2
> fullElectFrequency 4
> stepspercycle 20
>
> # Constant Temperature Control
> langevin off ;# do langevin dynamics
> langevinDamping 1 ;# damping coefficient (gamma) of 10/ps (5)
> langevinTemp $temperature
> langevinHydrogen no ;# don't couple langevin bath to hydrogens
>
> # use lighter damping now that system is equilibrated
> # 0 para NVT 1 para NPT
> if {0} {
> langevinPiston on
> langevinPistonTarget 1.01325
> langevinPistonPeriod 200
> langevinPistonDecay 100
> langevinPistonTemp $temperature
> }
>
> #useGroupPressure yes # smaller fluctuations
> #useFlexibleCell yes # allow dimensions to fluctuate
> independently
> #useConstantRatio yes # fix shape in x-y plane
>
> # Periodic Boundary Conditions
> #cellBasisVector1 133.2 0.0 0.0
> #cellBasisVector2 0.0 132.3 0.0
> #cellBasisVector3 0.0 0.0 97.2
> #cellOrigin -0.38 -0.59 0.66
> # the z dimension is going to shrink so pad sufficiently
> # the margin could be reduced once the cell is equilibrated
> margin 3
>
> #wrapAll on
> #wrapNearest on
> # PME (for full-system periodic electrostatics)
> #PME yes
> #PMEGridSizeX 120
> #PMEGridSizeY 120
> #PMEGridSizeZ 120
>
>
> # Output
> binaryoutput no
> outputEnergies 500
> outputTiming 500
> xstFreq 1000
> dcdFreq 1000
> restartfreq 1000
>
> ############################################
>
> if {1} {
> fixedAtoms on
> fixedAtomsForces yes
> fixedAtomsFile fix.pdb
> fixedAtomsCol B
> }
>
>
> ############################################
>
> if {0} {
> constraints on
> consRef restrain_CA.pdb
> consKFile restrain_CA.pdb
> consKCol B
> }
>
> # IMD Settings (can view sim in VMD)
> if {0} {
> IMDon on
> IMDport 3000 ;# port number (enter it in VMD)
> IMDfreq 1 ;# send every 1 frame
> IMDwait no ;# wait for VMD to connect before running?
> }
>
>
> #############################################################
>
>
> #############################################################
>
> # run one step to get into scripting mode
> minimize 0
> # turn off until later
> langevinPiston off
> #fixedAtoms off
> # minimize nonbackbone atoms
>
>
> minimize 5000
> output min_fixBB_vacio
> run 250000
>
>
>
>

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