From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon Oct 28 2013 - 16:28:15 CDT
Hello Max, the distances are not necessarily calculated by VMD using the
minimum image convention: can you use temporarily forceNoPBC yes in the
colvars input to see if this is a PBC problem?
Giacomo
On Mon, Oct 28, 2013 at 5:21 PM, Maximilian Ebert <max.ebert_at_me.com> wrote:
> Dear list,
>
> I am running an ABF experiment using NAMD and the FF AMBER99SB-ildn. My
> colvars definition is added to the end of this email.
>
> The atom numbers are the same as in the PDB file exported from tleap while
> preparing the system. After running the simulation I have the impression
> that I picked the wrong atom numbers. I imported the trajectory to VMD and
> exported the distances between the two atoms (I took into account that VMD
> starts at zero so that the distance is actually between 7426 and 7363). The
> distances do not match with the distances in the colvars.traj file. Is
> there any possibility to verify which atoms where really picked during the
> simulation? Since AMBER doesn’t use a PDB file as input in NAMD there is
> always the possibility that the atom numbering is wrong.
>
> Thank you very much,
>
> Max
>
>
> colvarsTrajFrequency 10000
> colvarsRestartFrequency 10000
>
> colvar {
> name AtomDistance
>
> width 0.5
>
> lowerboundary 3.0 ;# minimal distance
> upperboundary 32.5 ;# maximal distance
>
> lowerwallconstant 10.0 ;# provides the force
> constant. The energy unit of the constant is kcal/mol, while the spatial
> unit is that of the colvar.
> upperwallconstant 10.0 ;# same
>
> distance {
> group1 {
> atomnumbers { 7427 }
> }
> group2 {
> atomnumbers { 7364 }
> }
> }
> }
>
>
> abf {
> colvars AtomDistance
> fullSamples 500 ;# Number of samples in a
> bin prior to application of the ABF
> hideJacobian
> }
>
>
>
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