Re: Umbrella sampling using dihedral angle

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue Jan 24 2012 - 09:38:30 CST

Hello Maiti, if you only want positive values of the dihedral for output
purposes, you can use wrapAround 180. Is that what you need?

On Sun, Jan 22, 2012 at 11:17 PM, Buddhadev Maiti <bmaiti_at_gsu.edu> wrote:

> 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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