From: naresh kumar (naresh.cmds_at_gmail.com)
Date: Thu Apr 10 2014 - 12:54:02 CDT
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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