From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Sun Jan 26 2014 - 15:37:10 CST
Hello Magnus, first of all, you're doing an ABF calculation with different
windows, not a steered MD calculation.
Secondly, you have a relatively large force constant (100 kcal/mol/Å^2):
have you tried using a lower one or disabling it, to see whether it's that
restraint force or the ABF force the culprit?
Third, some care should be taken when wrapping coordinates (see paragraph
in the colvars section of the users's guide): does your NAMD configuration
e.g. make use of wrapAll?
Giacomo
On Sat, Jan 25, 2014 at 12:02 PM, Magnus Andersson <
magnus.andersson_at_scilifelab.se> wrote:
> Hi,
>
> I have equilibrated my system (membrane protein) and have performed a
> steered MD (moving ligand through channel).
>
> But, the simulations of each of the windows along the reaction coordinate
> crash immediately:
>
> ERROR: Constraint failure; simulation has become unstable.
> ERROR: Constraint failure in RATTLE algorithm for atom 11603!
>
> The atom is a hydrogen atom on a lipid. This lipid is at the edge of the
> box. I have checked this visually - I see nothing strange in this region
> (i.e. no clashes or strained geometries). When I increase the box size, it
> still crashes but with different atoms.
>
> I'm minimizing for 10,000 steps before starting the PMF simulation. I have
> also tried equilibrating for 2 more ns (i.e. without colvars), but get
> crash as soon as I turn colvars on.
>
> Decreasing the time step does not help either. Or margin. Or changing the
> reference atoms in the colvars file.
>
> Does anyone have an idea of what might be going on?
>
> Some features from the input file:
>
> stepspercycle 20
> rigidBonds all
> fullElectFrequency 4
> nonbondedFreq 2
>
> exclude scaled1-4
> 1-4scaling 1.0
> switching on
> vdwForceSwitching yes
> switchdist 10.0
> cutoff 12.0
> pairlistdist 13.5
>
> colvars on
> colvarsConfig restrain.in
>
> langevin on
> langevinDamping 5
> langevinTemp 310
>
> useGroupPressure yes
> useFlexibleCell yes
> LangevinPiston on
> LangevinPistonTarget 1.0
> LangevinPistonPeriod 200
> LangevinPistonDecay 100
> LangevinPistonTemp 310
>
> The colvars file:
>
> colvarsTrajFrequency 1000
> colvarsRestartFrequency 1000
>
> colvar {
> name Translocation
> width 0.1
> lowerboundary 37
> upperboundary 38
> lowerwallconstant 100.0
> upperwallconstant 100.0
> distanceZ {
> main {
> atomnumbers { 59035 }
> }
>
> ref {
> atomnumbers { (here I use all CA in the transmembrane
> section of the protein }
> }
> axis ( 0.0, 0.0, 1.0 )
> }
> }
> abf {
> colvars Translocation
> fullSamples 1000
>
> Cheers,
>
> Magnus
>
>
>
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