From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue Feb 25 2014 - 20:19:28 CST
Hello Maria, there could be a few issues at play:
1) possible discontinuity in the colvar's value because one or more atoms
has been wrapped (see section in the user's guide about wrapping);
2) the system is out of equilibrium of its own regardless of the colvar
biasing potentials.
Giacomo
On Tue, Feb 25, 2014 at 12:02 PM, Maria Pikoula
<maria.pikoula_at_eng.ox.ac.uk>wrote:
> Dear all,
>
> In my simulation of two GlcNS(6S) restrained close to each other using
> ABF, the simulation fails at at some point, usually after 10 or more
> nanoseconds. I get the following error:
>
> FATAL ERROR: Low global exclusion count! (9601 vs 9603) System unstable
> or pairlistdist or cutoff too small.
>
> Increasing the pairlistdist hasn't helped. Any ideas what may be causing
> this? Below I copy the configuration file and the colvars input file.
>
> Regards,
>
> Maria
>
> Config. File:
> #############################################################
> ## SIMULATION PARAMETERS ##
> #############################################################
> coordinates eqlb.coor
> margin 30;
> numsteps 25000000
> set temp 300
> set outputname abf_3.7to10
>
> firsttimestep 0
>
> binaryoutput no
> binaryrestart no
>
>
> velocities eqlb.vel
>
> paraTypeCharmm off
>
> amber on
> parmfile ../monomers_WAT.prmtop
>
> # Force-Field Parameters
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 12.
> switching off
> pairlistdist 13.5
>
>
> # Integrator Parameters
> timestep 2
> rigidBonds all
> nonbondedFreq 1
> fullElectFrequency 2
> stepspercycle 10
>
>
> # Constant Temperature Control Using Berendsen Method (Coupling)
>
> tCouple on
> tCoupleTemp $temp
> tCoupleFile temp_coupling.pdb
> tCoupleCol B
>
> wrapAll off
>
> extendedSystem eqlb.xsc
>
> # PME (for full-system periodic electrostatics)
> PME yes
> PMEGridSpacing 1.0
>
> # Constant Pressure Control (variable volume)
> useGroupPressure yes
> useFlexibleCell no
> useConstantArea no
>
> BerendsenPressure on
> BerendsenPressureTarget 1.01325 ;# in bar -> 1 atm
> BerendsenPressureCompressibility 4.57E-5
> BerendsenPressureRelaxationTime 100
> BerendsenPressureFreq 10
>
>
> # Output
> outputName $outputname
>
>
> restartfreq 500
> dcdfreq 250
> xstFreq 250
> outputEnergies 100
> outputPressure 100
>
> colvars on
> colvarsConfig Distance_3.7to10.in
>
> ##############################################
>
> Colvars file:
>
> ##############################################
>
> colvarsTrajFrequency 250
> colvarsRestartFrequency 20000
>
> colvar {
> name AtomDistance
> outputAppliedForce on
> width 0.1
>
> lowerboundary 3.7
> upperboundary 10.0
>
> lowerwallconstant 10.0
> upperwallconstant 10.0
>
> distance {
> group1 {
> atomnumbers { 8 16 }
> }
> group2 {
> atomnumbers { 42 50 }
> }
> }
> }
>
>
> abf {
> colvars AtomDistance
> fullSamples 1000
> hideJacobian
> }
> ##############################################
>
> Maria Pikoula
> Doctoral Candidate in Centre for Doctoral Training in Healthcare Innovation
> Institute of Biomedical Engineering
> Department of Engineering Science
> University of Oxford
> maria.pikoula_at_eng.ox.ac.uk
>
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