Umbrella sampling using dihedral angle

From: Buddhadev Maiti (bmaiti_at_gsu.edu)
Date: Sun Jan 22 2012 - 22:17:25 CST

Dear Giacomo,

Thank you very much for your all kind of great help. Finally I decided to do umbrella sampling using dihedral angle. I have another question. I would like to print positive value of dihedral angle in us1.colvars.traj, could you please reply me what kind of option do I need to put in namd configuration file.

Have a nice day,

Thanks,

Maiti

covarsconfig:

Colvarstrajfrequency 100

Colvarsrestartfrequency 100

colvar {

name us

dihedral {

group1 {

atomnumbers { 3639 3640 3642 3644 3645 3646 3648 3649 }

}

group2 {

atomnumbers { 3634 3636 3637 3650 3652 3655 3656 3657 3658 3659 }

}

group3 {

atomnumbers { 3663 3665 3666 3682 3684 3687 3688 3689 3690 3691 }

}

group4 {

atomnumbers { 3668 3669 3671 3672 3673 3674 3678 3677 3680 3681 }

}

}

}

harmonic {

colvars us

centers -1.70350780500746e+02

forceConstant 10.0

}

us1.colvars.traj:

# step us

0 -1.78341424821100e+02

100 -1.78341417695444e+02

200 -1.78341427134217e+02

300 -1.78341453149846e+02

But I like to print this way:

# step us

0 1.78341424821100e+02

100 1.78341417695444e+02

200 1.78341427134217e+02

300 1.78341453149846e+02

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