From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon Nov 21 2016 - 11:10:57 CST
Hi Bala, to enforce a strict boundary would be very difficult, because it
would eventually lead to discontinuous forces.
One thing to watch for with distanceZ as well as all other distance-based
variables is how the PBCs affect the result. I can't say that there is any
problem based on what you're saying, however watch for jumps between
positive and negative values, too.
Giacomo
On Sat, Nov 19, 2016 at 11:12 AM, Karteek Bejagam <karteek4_at_vt.edu> wrote:
> Hi,
>
> I think 0.32 A crossing the boundary is not a problem. It depends on the
> wall force constant. Since it adds half harmonic beyond the wall.
>
> Hope this helps.
>
> Best,
> Karteek
> Dept. of Chemical Engineering,
> VirginiaTech, Blacksburg.
>
> On Sat, Nov 19, 2016 at 9:18 AM, Bala subramanian <
> bala.biophysics_at_gmail.com> wrote:
>
>> Friends,
>> My objective is to restrain an ion-A within a Z-distance of 6.5Ang from
>> ion-B. I defined the colvar as below. I dnt apply any other bias on ion-A
>>
>> colvar {
>> name LONGI
>> width 0.5
>> upperboundary 0.0
>> lowerboundary -6.5
>>
>> lowerwallconstant 100.0
>> upperwallconstant 100.0
>>
>> distanceZ {
>> main {
>> atomnumbers { 16628 } ; ion-A
>> }
>> ref {
>> atomnumbers { 16625 } ; ion-B ( Z of B > Z of A)
>> }
>> axis ( 0.0, 0.0, 1.0 )
>> }
>> }
>>
>> When i analysed the colvar.traj, i see that the distanceZ varying -6.82
>> to -4.10. I wonder how when i fix the distanceZ to be within -6.5Ang, it
>> increase up to -6.82 ?. Is it normal ?. Do i need to use any other criteria
>> to achieve distanceZ to be strictly within -6.5.
>>
>> --
>> C. Balasubramanian
>>
>
>
-- Giacomo Fiorin Associate Professor of Research Institute for Computational Molecular Science (ICMS) College of Science and Technology, Temple University 1925 North 12th Street (035-07), Room 704D Philadelphia, PA 19122-1801 Phone: +1-215-204-4213 Scholar: http://goo.gl/Q3TBQU Personal: http://giacomofiorin.github.io/ Lab page: https://icms.cst.temple.edu/members.html *"As computer programmers we have a responsibility to make sure that we run the computers instead of the computers running us."* - Steve Oualline
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