TARGETED MD ERROR

From: Samuel Morales Navarro (samue_82_at_hotmail.com)
Date: Wed Mar 12 2008 - 13:33:56 CDT

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

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:49:19 CST