Re: TARGETED MD ERROR

From: mon_sharma_at_research.iiit.ac.in
Date: Thu Mar 13 2008 - 01:52:57 CDT

Hii. I think the error says it all. U r using two modes of temperature
control- langevin and temperature coupling. Try using either of them, or
there is any specific reason for that. If TMD is an aspect of SMD, so I
think u need not use temperature control.

Regards,
Monika
  On Wed, 12 Mar 2008, Samuel Morales Navarro wrote:

> Hi NAMD users!!.
>
>
>
> In Targeted MD in vacuo , and I appeared the following error:
>
>
>
> Reason: FATAL ERROR: Langevin dynamics and temperature coupling are mutually
> exclusive dynamics modes
>
> why?
>
> I attached my TMD configuration file in NAMD
>
>
>
> # Input
>
> paraTypeCharmm on
>
> parameters par_all27_prot_lipid.inp
>
>
>
> #temperature $temperature
>
>
>
>
>
> firsttimestep 0
>
>
>
>
>
> # Force-Field Parameters
>
> exclude scaled1-4
>
> 1-4scaling 1.0
>
> cutoff 12.
>
> switching on
>
> switchdist 10.
>
> pairlistdist 13.5
>
>
>
> # Integrator Parameters
>
> timestep 1.0 ;# 1fs/step (2)
>
> rigidBonds water ;# needed for 1fs steps (2)
>
> nonbondedFreq 2
>
> fullElectFrequency 4
>
> stepspercycle 20
>
>
>
> #cellBasisVector1 82.00 00.00 00.00
>
> #cellBasisVector2 00.00 82.00 00.00
>
> #cellBasisVector3 00.00 00.00 82.00
>
> #cellOrigin 0.0 0.0 0.0
>
>
>
> #Pme on
>
> #PmeGridsizeX 82
>
> #PmeGridsizeY 82
>
> #PmeGridsizeZ 82
>
>
>
> #useGroupPressure yes # smaller fluctuations
>
> #useFlexibleCell no # allow dimensions to fluctuate
> independently
>
> #useConstantRatio no # fix shape in x-y plane
>
>
>
> #margin 2.5
>
>
>
> #wrapAll on
>
>
>
>
>
>
> #Output
>
> binaryoutput no
>
> outputEnergies 1000
>
> outputTiming 1000
>
> xstFreq 1000
>
> dcdFreq 1000
>
> restartfreq 1000
>
>
>
> langevin on
>
> langevinDamping 10
>
> langevinTemp 300
>
> langevinHydrogen on
>
>
>
> #langevinPiston on
>
> #langevinPistonTarget 1.01325 ;# in bar -> 1 atm
>
> #langevinPistonPeriod 100.
>
> #langevinPistonDecay 50.
>
> #langevinPistonTemp 300
>
>
>
>
>
> ############################################
>
>
>
> #if {1} {
>
>
>
> #fixedAtoms on
>
> #fixedAtomsForces yes
>
> #fixedAtomsFile fixed_pot_cargada.pdb
>
> #fixedAtomsCol B
>
>
>
> #}
>
> #pwd
>
>
>
> ############################################
>
>
>
> if {0} {
>
>
>
> constraints on
>
> consRef restrain.pdb
>
> consKFile restrain.pdb
>
> consKCol B
>
>
>
> }
>
>
>
> # Temperature control
>
> tCouple on
>
> tCoupleTemp 300
>
> tCoupleFile tcouple.coor
>
>
>
> #parametros del TMD
>
> TMD on
>
> TMDk 200
>
> TMDoutputFreq 1
>
> TMDFile closed.pdb
>
> TMDFirststep 0
>
> TMDLaststep 100000
>
> TMDInitialRMSD 8.37
>
> TMDFinalRMSD 0
>
>
>
>
>
> run 100000;
>
>
>
> Thanks for yours help,
>
> _______________________________
>
> Samuel Morales Navarro
>
> Licenciado en Bioquímica
>
> Pontificia Universidad Católica de Chile
>
> Centro de Bioinformática y Simulación Molecular
>
> Universidad de Talca
>
> <http://cbsm.utalca.cl/> http://cbsm.utalca.cl/
>
>
>
> "...For God so loved the world that he gave his one and only Son, that
> whoever believes in him shall not perish but have eternal life..." John 3.16
>
>
>
>

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