From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Tue Sep 13 2011 - 05:43:39 CDT
Hi Alex,
It's very difficult to say just from this. Did both simulations sample
the colvar space well? what do the histograms look like?
Jerome
On 13 September 2011 12:13, Alex <alniagap_at_gmail.com> wrote:
> Hi,
> I have got different free energy surfaces obtained by using adaptive
> biasing force method and metadyanmics calculations for the same
> molecule (paracetamol) in vacuum. Could you explain to me why? The
> duration of the simulated trajectory was 25 ns after equilibration.
> Difference between configurations of calculations only in colvars
> configurations.
>
> ABF colvars config contains lines like these:
> ##################################################
> colvarsTrajFrequency 500
> colvarsRestartFrequency 500
> colvar {
> name phi
> width 5.0
> lowerboundary -180
> upperboundary 180
> dihedral {
> oneSiteSystemForce
> group1 {
> atomnumbers 6
> }
> group2 {
> atomnumbers 5
> }
> group3 {
> atomnumbers 7
> }
> group4 {
> atomnumbers 9
> }
> }
> }
> colvar {
> name psi
> width 5.0
> lowerboundary -180
> upperboundary 180
> dihedral {
> oneSiteSystemForce
> group1 {
> atomnumbers 5
> }
> group2 {
> atomnumbers 7
> }
> group3 {
> atomnumbers 9
> }
> group4 {
> atomnumbers 10
> }
> }
> }
> abf {
> colvars phi psi
> fullSamples 200
> }
> ##################################################
>
> Metadynamics colvars config contains lines like these:
> ##################################################
> colvarsTrajFrequency 500
> colvarsRestartFrequency 500
> colvar {
> name phi
> width 5.0
> lowerboundary -180
> upperboundary 180
> dihedral {
> oneSiteSystemForce
> group1 {
> atomnumbers 6
> }
> group2 {
> atomnumbers 5
> }
> group3 {
> atomnumbers 7
> }
> group4 {
> atomnumbers 9
> }
> }
> }
> colvar {
> name psi
> width 5.0
> lowerboundary -180
> upperboundary 180
> dihedral {
> oneSiteSystemForce
> group1 {
> atomnumbers 5
> }
> group2 {
> atomnumbers 7
> }
> group3 {
> atomnumbers 9
> }
> group4 {
> atomnumbers 10
> }
> }
> }
> metadynamics {
> colvars phi psi
> hillWidth 2
> }
> ##################################################
>
> Where phi and psi is the dihedral angles.
>
> Simulations config contains lines like these:
> ##################################################
> numSteps 50000000
> structure system.psf
> coordinates system.pdb
> set temperature 313
> set outputname out_system_1
> set inputname out_system
> binCoordinates $inputname.coor
> binVelocities $inputname.vel
> firsttimestep 0
> paraTypeCharmm on
> parameters par_all36_cgenff.prm
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 14.0
> switching on
> switchdist 10.0
> pairlistdist 18.5
> timestep 0.5
> rigidBonds none
> nonbondedFreq 1
> fullElectFrequency 2
> stepspercycle 10
> langevin on
> langevinDamping 5
> langevinTemp $temperature
> langevinHydrogen on
> wrapAll on
> outputName $outputname
> restartfreq 500
> dcdfreq 500
> xstFreq 500
> outputEnergies 500
> outputPressure 500
> colvars on
> colvarsConfig colvars.in
> ##################################################
>
> Equilibrations config contains lines like these:
> ##################################################
> structure system.psf
> coordinates system.pdb
> set temperature 313
> set outputname out_system
> firsttimestep 0
> paraTypeCharmm on
> parameters par_all36_cgenff.prm
> temperature $temperature
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 14.0
> switching on
> switchdist 10.0
> pairlistdist 18.5
> timestep 0.5
> rigidBonds none
> nonbondedFreq 1
> fullElectFrequency 2
> stepspercycle 10
> langevin on
> langevinDamping 5
> langevinTemp $temperature
> langevinHydrogen on
> wrapAll on
> outputName $outputname
> restartfreq 500
> dcdfreq 500
> xstFreq 500
> outputEnergies 500
> outputPressure 500
> minimize 500
> reinitvels $temperature
> run 10000000
> ##################################################
>
> PDB file of the molecule:
> ###############################################################################
> ATOM 1 C14 PACP 1 16.078 10.242 15.441 1.00 0.00 PACP C
> ATOM 2 H141 PACP 1 16.509 10.274 14.677 1.00 0.00 PACP H
> ATOM 3 H142 PACP 1 16.407 10.180 16.325 1.00 0.00 PACP H
> ATOM 4 H143 PACP 1 15.840 11.289 15.469 1.00 0.00 PACP H
> ATOM 5 C15 PACP 1 14.790 9.463 15.330 1.00 0.00 PACP C
> ATOM 6 O29 PACP 1 13.986 9.378 16.260 1.00 0.00 PACP O
> ATOM 7 N21 PACP 1 14.595 8.870 14.144 1.00 0.00 PACP N
> ATOM 8 H211 PACP 1 15.297 8.939 13.578 1.00 0.00 PACP H
> ATOM 9 C22 PACP 1 13.511 8.034 13.744 1.00 0.00 PACP C
> ATOM 10 C23 PACP 1 12.251 8.048 14.333 1.00 0.00 PACP C
> ATOM 11 H231 PACP 1 12.091 8.657 15.016 1.00 0.00 PACP H
> ATOM 12 C24 PACP 1 11.251 7.197 13.873 1.00 0.00 PACP C
> ATOM 13 H241 PACP 1 10.346 7.257 14.243 1.00 0.00 PACP H
> ATOM 14 C26 PACP 1 12.755 6.339 12.207 1.00 0.00 PACP C
> ATOM 15 H261 PACP 1 12.920 5.762 11.471 1.00 0.00 PACP H
> ATOM 16 C27 PACP 1 13.742 7.183 12.672 1.00 0.00 PACP C
> ATOM 17 H271 PACP 1 14.614 7.182 12.269 1.00 0.00 PACP H
> ATOM 18 C25 PACP 1 11.503 6.336 12.818 1.00 0.00 PACP C
> ATOM 19 O28 PACP 1 10.485 5.500 12.416 1.00 0.00 PACP O
> ATOM 20 H281 PACP 1 10.673 5.217 11.599 1.00 0.00 PACP H
> END
> ###############################################################################
>
> --
> with best regards,
> Alex
>
>
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