From: Maria Pikoula (maria.pikoula_at_eng.ox.ac.uk)
Date: Fri Feb 28 2014 - 11:42:47 CST
Dear Thanassis,
Thanks for your comments and input. I reset the margin to 0 and I am still getting the same issue. I don't think the problem is a non-equilibrated system either. Do you think I should just restart every time it happens then?
Cheers,
Maria
On 25 Feb 2014, at 17:15, Athanassios Stavrakoudis wrote:
>
> Hi,
>
> Setting margin to 30 is a bad idea.
> Better keep it close to zero.
> It might be a poorly equilibrated system.
> Anyway you can restart your simulation from the point it stopped.
> Afterwards you can merge your dcd files.
>
> Best,
> Thanassis
>
>
>> 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
>>
>
>
>
> --
> Athanassios Stavrakoudis
> University of Ioannina web: http://stavrakoudis.econ.uoi.gr/
> Department of Economics e-mail: mailto:astavrak_at_uoi.gr
> GR-45110, Ioannina tel: +30 265 100 5935
> GREECE fax: +30 265 100 5092
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
This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:22:11 CST