From: Kevin C Chan (cchan2242-c_at_my.cityu.edu.hk)
Date: Wed Nov 26 2014 - 20:32:24 CST
Dear Jerome,
Thanks for the hint. I thought about PBC at first but I measured my box wrongly so I could not get to the answer. It turns out to be a problem with PBC and that is why we have the forceNoPBC option.
Regards,
Kevin
> On 26 Nov, 2014, at 21:35, Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:
>
> 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 <mailto: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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