From: naresh kumar (naresh.cmds_at_gmail.com)
Date: Mon Apr 14 2014 - 10:11:37 CDT
hi Giacomo,
Thanks for the information. It works perfectly now.
Thanks,
Naresh
2014-04-11 19:49 GMT+02:00 Giacomo Fiorin <giacomo.fiorin_at_gmail.com>:
> 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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