From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Wed Nov 26 2014 - 07:35:37 CST
That looks like a PBC issue. What is the minimum-image distance between
your groups?
Jerome
On 26 November 2014 at 14:25, Kevin C Chan <cchan2242-c_at_my.cityu.edu.hk>
wrote:
> Thanks Jerome for your suggestion. I have read the documentation. So would
> you like to explain how can we get the -65 from 40 and -55?
>
> Regards,
> Kevin
>
>
> On 26 Nov, 2014, at 19:07, Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:
>
> Hi Kevin,
>
> Please read the documentation for the distanceZ component.
>
> Jerome
>
> On 26 November 2014 at 04:03, Kevin C Chan <cchan2242-c_at_my.cityu.edu.hk>
> wrote:
>
>> Dear Users,
>>
>> I am currently using DistanceZ for my colvars definition and everything
>> goes fine except it does not gives me the value I expect.
>>
>> I thought DistanceZ was measuring the subtracted vector between the
>> centre of mass of atoms in the main group and that in the ref group and
>> then projected it onto the z-axis, in other words only the z component is
>> of the interest. In my system,
>> com of main locates at z=40
>> com of ref locates at z=-55
>> However the first step (step 0) of colvars.traj gives me -65 for
>> DistanceZ.
>>
>> As I'm doing the umbrella sampling, it's fine if I change my windows list
>> according to z=-65 but I'm just curious what DistanceZ was actually
>> measuring.
>>
>> Thanks in advance,
>> Kevin
>> ukevi_at_gmx.hk
>>
>> Follow is the input parameters:
>>
>> colvar {
>> name ProjectionZ
>>
>> width 0.25
>>
>> distanceZ {
>>
>> main {
>> atomsFile main.pdb
>> atomsCol B
>> atomsColValue 1.0
>> }
>> ref {
>> atomsFile ref.pdb
>> atomsCol B
>> atomsColValue 1.0
>> }
>> }
>> }
>>
>> harmonic {
>> colvars ProjectionZ
>> centers 40
>> forceConstant 4.0
>> }
>>
>>
>
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