From: naresh kumar (naresh.cmds_at_gmail.com)
Date: Fri Apr 11 2014 - 12:01:32 CDT
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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