From: Z (shenzldlut_at_gmail.com)
Date: Mon Oct 06 2014 - 07:02:28 CDT
OK!Thank you!
This is my configuration file:
structure mem_50.psf
coordinates mem_50.pdb
set outputname mem_50
set temperature 300
# Input
paraTypeCharmm on
parameters par_all27_prot_lipid.prm
temperature $temperature
# Periodic Boundary conditions
cellBasisVector1 55.0 0.0 0.0
cellBasisVector2 0.0 55.0 0.0
cellBasisVector3 0.0 0.0 95.0
wrapWater on
wrapAll on
margin 3
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 10.
pairlistdist 14.5
# Integrator Parameters
timestep 1
nonbondedFreq 2
fullElectFrequency 4
stepspercycle 20
#PME
PME yes
PMEGridSpacing 1.0
# Constant Temperature Control
langevin on
langevinDamping 5
langevinTemp $temperature
langevinHydrogen no
# Constant Pressure Control
if {1} {
useGroupPressure yes
useFlexibleCell no
useConstantArea no
langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 1000.0
langevinPistonDecay 500.0
langevinPistonTemp $temperature
}
# Output
outputName $outputname
restartfreq 1000 ;# 500steps = every 1ps
dcdfreq 1000
outputEnergies 1000
outputPressure 1000
rigidBonds all
rigidTolerance 0.0005
# Fixed Atoms Constraint (set PDB beta-column to 1)
if {1} {
fixedAtoms on
fixedAtomsFile mem_fix.pdb
fixedAtomsCol B
}
#############################################################
## EXTRA PARAMETERS ##
#############################################################
if {1} {
tclForces on
set waterCheckFreq 10
set allatompdb mem_50.pdb
tclForcesScript addforce.tcl
}
if {1} {
tclBC on
tclBCScript {
set sphereCenter "0.0 0.0 0.0"
set sphereRadius 10.0
set maxForce 5.0
set pdbSource mem_50.pdb
set tclBCScript force.tcl
source $tclBCScript
}
}
if {1} {
minimize 1000
reinitvels $temperature
}
colvars on
colvarsConfig Distance.in
firsttimestep 22000
run 2000000
Z
E-mail：shendlut_at_gmail.com
在 2014/10/6 19:27, Giacomo Fiorin 写道:
>
> Looks like the NAMD keyword isn't being recognized properly. It would
> be better to look at the entire NAMD configuration file.
>
> On Oct 6, 2014 6:54 AM, "Z" <shenzldlut_at_gmail.com
> <mailto:shenzldlut_at_gmail.com>> wrote:
>
> The colvars configuration as a separate file(.in format).In my
> NAMD config file ,the colvers is been written like this:
>
> colvars on
> colvarsConfig Distance.in
>
> firsttimestep 22000
> run 2000000
>
> Z
> E-mail：shendlut_at_gmail.com <mailto:shendlut_at_gmail.com>
>
> 2014/10/6 18:45, Giacomo Fiorin:
>>
>> Do you supply the colvars configuration as a separate file or as
>> part of the NAMD configuration file?
>>
>> On Oct 6, 2014 6:26 AM, "Z" <shenzldlut_at_gmail.com
>> <mailto:shenzldlut_at_gmail.com>> wrote:
>>
>> Dear all,
>> I want to use ABF to calculate PMF,so I am running simulation
>> with colvars. However, the NAMD2.8 said :
>>
>> TCL: Setting parameter colvars to on
>> FATAL ERROR: Setting parameter colvars from script failed!
>>
>> FATAL ERROR: Setting parameter colvars from script failed!
>>
>> FATAL ERROR: Setting parameter colvars from script failed!
>>
>> FATAL ERROR: Setting parameter colvars from script failed!
>>
>> FATAL ERROR: Setting parameter colvars from script failed!
>>
>> my colvars flie :
>> colvarsTrajFrequency 100
>> colvarsRestartFrequency 1000
>>
>> colvar {
>> name IonDistance
>>
>> width 0.1
>>
>> lowerboundary -45.6
>> upperboundary 45.6
>>
>> lowerWallConstant 10.0
>> upperWallConstant 10.0
>>
>> distanceZ {
>> main {
>> atomsFile ./main_atom.pdb
>> atomsCol B
>> atomsColValue 1.0
>> }
>> ref {
>> atomsFile ./ref_atom_2.pdb
>> atomsCol O
>> atomsColValue 1.0
>> }
>> }
>> }
>>
>> abf {
>> colvars IonDistance
>> fullSamples 100
>> hideJacobian
>> }
>>
>> I want to know which parameter has problem?
>> Thanks!
>>
>> P.S.
>> There are tclForces parameters in my conf flie.
>>
>> --
>> Z
>> E-mail：shendlut_at_gmail.com <mailto:shendlut_at_gmail.com>
>>
>
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