From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Fri Apr 11 2014 - 12:49:20 CDT
Naresh: distanceZ and distanceXY must be defined using the same axis for
consistent use.
Giacomo
On Fri, Apr 11, 2014 at 1:01 PM, naresh kumar <naresh.cmds_at_gmail.com> wrote:
> Hi,
> Thanks for the reply. I understand that the axis are
> different. My doubt is in what way it will affect the force acting on the
> cation making it not to remain in the cylinder.
> Could you please kindly expalin how it will affect the force acting on the
> cation.
>
> Thanks in advance
>
> Sincerely,
> Naresh
>
>
> 2014-04-10 21:06 GMT+02:00 Giacomo Fiorin <giacomo.fiorin_at_gmail.com>:
>
> The problem is that:
>>
>> axis {
>> (0.0, 0.0, -1.0)
>> }
>>
>> is different from:
>>
>> axis {
>> (1.0, 1.0, 0.0)
>> }
>>
>>
>>
>> On Thu, Apr 10, 2014 at 1:54 PM, naresh kumar <naresh.cmds_at_gmail.com>wrote:
>>
>>> Hi Giacomo,
>>> Thanks for the reply. But i couldn't understand what you
>>> mean. Could you please kindly explain.
>>>
>>> Thanks,
>>> Naresh
>>>
>>>
>>> 2014-04-10 19:03 GMT+02:00 Giacomo Fiorin <giacomo.fiorin_at_gmail.com>:
>>>
>>> Hello Naresh you should define the same axis for both variables.
>>>>
>>>> Giacomo
>>>> On Apr 10, 2014 12:37 PM, "naresh kumar" <naresh.cmds_at_gmail.com> wrote:
>>>>
>>>>> Hi all,
>>>>> I am using Collective Variable module in NAMD to get the free
>>>>> energy profiles. I have been using the colvars module in NAMD extensively
>>>>> for our work.
>>>>>
>>>>> I am trying to calculate the free energy profile of a cation along the
>>>>> normal to a specific site (COM of six atoms) on a solid substrate. Hence, i
>>>>> used distance Z and distance XY component for the CV analysis using
>>>>> harmonic constraints only for the distance Z components and for distance XY
>>>>> i have set the harmonic forceconstant to 0, but have applied lower and
>>>>> upper wall/boundary with force constant.
>>>>>
>>>>> I think in this way, the ion would explore a cylinder along the normal
>>>>> to the solid surface. Below is the config file i used for performing
>>>>> colvars module. The simulation runs fine without any issues.
>>>>>
>>>>> colvar {
>>>>> name pmf-dist
>>>>> width 0.4
>>>>> lowerboundary 1.0
>>>>> upperboundary 15.0
>>>>> expandboundaries off
>>>>>
>>>>> ###################### Component section ############################
>>>>> distanceZ {
>>>>> main {
>>>>> atomNumbers 3975
>>>>> }
>>>>> ref {
>>>>> atomNumbers 1384 1383 1374 1378 2262 2294
>>>>> }
>>>>> axis {
>>>>> (0.0, 0.0, -1.0)
>>>>> }
>>>>> forceNoPBC no
>>>>> oneSiteSystemForce no
>>>>> }
>>>>> outputValue on
>>>>> outputVelocity off
>>>>> outputSystemForce on
>>>>> outputAppliedForce on
>>>>> }
>>>>>
>>>>> colvar {
>>>>>
>>>>> name pmf-dist-xy
>>>>> width 0.4
>>>>>
>>>>> lowerboundary 0.0
>>>>> upperboundary 0.5
>>>>> expandboundaries off
>>>>> #lowerwall 0.0
>>>>> #lowerwallconstant 0.0
>>>>> upperwall 0.5
>>>>> upperwallconstant 0.7
>>>>>
>>>>> ###################### Component section ############################
>>>>>
>>>>> distanceXY {
>>>>> main {
>>>>> atomNumbers 3975
>>>>> }
>>>>> ref {
>>>>> atomNumbers 1384 1383 1374 1378 2262 2294
>>>>> }
>>>>> axis {
>>>>> (1.0, 1.0, 0.0)
>>>>> }
>>>>> forceNoPBC no
>>>>> oneSiteSystemForce no
>>>>> }
>>>>> outputValue on
>>>>> outputVelocity off
>>>>> outputSystemForce on
>>>>> outputAppliedForce on
>>>>> }
>>>>>
>>>>> harmonic {
>>>>> name umbrella-z
>>>>> colvars pmf-dist
>>>>> forceConstant 4.0
>>>>> centers 2.8
>>>>> }
>>>>> harmonic {
>>>>> name umbrella-xy
>>>>> colvars pmf-dist-xy
>>>>> forceConstant 0.0
>>>>> centers 0.0
>>>>> }
>>>>>
>>>>> However, when i view the trajectory file (dcd), the ion moves outside
>>>>> the boundary and wall constraints along XY and nevers comes back inside the
>>>>> cylinder. If i am correct, the term wall indicates a solid surface.
>>>>>
>>>>> My doubts are
>>>>> 1) why the ion is moving outside the wall eventhough there is a
>>>>> presence of upperwall force constant.
>>>>> 2) Does it indicate that the upperwall force constant value is not
>>>>> high enough to bring back the ion inside the cylinder. If that so, i have
>>>>> tried with high value but it is not working.
>>>>> 3) How can i probe the ion only inside the cylinder. Is there anything
>>>>> i am missing here.
>>>>>
>>>>> Could you please help me to solve the issue.
>>>>>
>>>>> Thanks in advance,
>>>>>
>>>>> Sincerely,
>>>>> Naresh
>>>>>
>>>>
>>>
>>
>
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