From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu Apr 10 2014 - 14:06:18 CDT
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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