Re: Colvars: Unable to restrict rotation and translation along y and z axes

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Fri May 20 2016 - 10:33:27 CDT

You can define the appropriate axis of symmetry for distanceXY: by default
it is (0, 0, 1).

On Fri, May 20, 2016 at 2:31 AM, Sourav Ray <souravray90_at_gmail.com> wrote:

> Hello Giacomo
>
> Thanks for the suggestion! I implemented "distanceXY" in my colvar module,
> I was able to restrict rotation and y-axis translation, but still was not
> able to restrict translation along z-axis, I presume I am not setting the
> "axis" option properly in "distanceXY" module or maybe I need to apply
> harmonic restraints to "distanceXY" also?
>
>
> colvarsTrajFrequency 10000
> colvarsRestartFrequency 10000
>
>
> colvar {
>
> name restxy
> width 0.1
> upperboundary 20.0
> upperwallconstant 1000.0
>
>
> distanceXY {
> ref {
> atomnumbersrange { 1-364 } # CNT1
> }
>
> main {
> atomnumbersrange { 365-728 } # CNT2
> }
> axis (0,1,1)
> }
> }
>
>
> colvar {
> name orient
> width 0.1 # distance between quaternions is from 0 to pi/2, so small
> fluctuations are significant
>
> orientation {
> atoms {
> atomNumbersrange { 1-728 }
> }
> refPositionsFile ../ref.pdb # Fetch initial positions from this
> file
> }
> }
>
>
> colvar {
> name xtrans
> width 0.1
> lowerboundary 12.0
> upperboundary 20.0
> lowerwallconstant 1000.0
> upperwallconstant 1000.0
>
> distanceZ {
> ref {
> atomnumbersrange { 1-364 } # CNT1
> }
>
> main {
> atomnumbersrange { 365-728 } # CNT2
> }
> axis (1,0,0)
> }
> }
>
>
> harmonic {
> colvars orient
> centers (1,0,0,0)
> forceconstant 100.0
> }
>
> metadynamics {
> colvars xtrans
> hillWidth 2
> hillWeight 0.5
> newHillFrequency 100
> }
>
> Regards
> Sourav
>
> On Fri, May 20, 2016 at 11:12 AM, Sourav Ray <souravray90_at_gmail.com>
> wrote:
>
>
>> ---------- Forwarded message ----------
>> From: Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
>> Date: Wed, May 18, 2016 at 6:53 PM
>> Subject: Re: namd-l: Colvars: Unable to restrict rotation and translation
>> along y and z axes
>> To: Sourav Ray <souravray90_at_gmail.com>, NAMD list <namd-l_at_ks.uiuc.edu>
>> Cc: Ajay Singh Panwar <panwar_at_iitb.ac.in>
>>
>>
>> Hello Sourav you probably want distancexy instead of distancedir?
>>
>> Giacomo
>> On May 18, 2016 8:53 AM, "Sourav Ray" <souravray90_at_gmail.com> wrote:
>>
>>> Hello
>>>
>>> I am trying to vary the distance between two carbon nanotubes along
>>> x-axis. Additionally, I would like to restrict any rotation, whatsoever,
>>> and translation along y and z axes. I am using "Distancedir" to restrict
>>> translation for both the nano-tubes along y and z axes and "orient" to
>>> restrict rotation with "harmonic" constraint. However, I am not getting the
>>> desired effect. Please find the colvars script below:
>>>
>>>
>>> colvarsTrajFrequency 10000
>>> colvarsRestartFrequency 10000
>>>
>>>
>>> colvar {
>>>
>>> name cntdis
>>> width 0.1
>>> lowerboundary 12.0
>>> upperboundary 20.0
>>> lowerwallconstant 100.0
>>> upperwallconstant 100.0
>>>
>>>
>>> distance {
>>> group1 {
>>> atomnumbersrange { 1-364 }
>>> }
>>>
>>> group2 {
>>> atomnumbersrange { 365-728 }
>>> }
>>>
>>> }
>>> }
>>>
>>> colvar {
>>> name orient
>>>
>>> width 0.1 # distance between quaternions is from 0 to pi/2, so small
>>> fluctuations are significant
>>>
>>> orientation {
>>> atoms {
>>> atomNumbersrange { 1-728 }
>>> enableForces off
>>> }
>>> refPositionsFile ../ref.pdb # Fetch initial positions from this
>>> file
>>> }
>>> }
>>>
>>>
>>> colvar {
>>>
>>> name ztrans1
>>> width 0.1
>>>
>>> distancedir {
>>> group1 {
>>> atomnumbersrange { 1-364 }
>>> }
>>>
>>> group2 {
>>> dummyatom (-6.5,0,0)
>>> }
>>> }
>>> }
>>>
>>> colvar {
>>>
>>> name ztrans2
>>> width 0.1
>>>
>>> distancedir {
>>> group1 {
>>> atomnumbersrange { 365-728 }
>>> }
>>>
>>> group2 {
>>> dummyatom (6.5,0,0)
>>> }
>>> }
>>>
>>>
>>> harmonic {
>>> colvars orient ztrans1 ztrans2
>>> centers (1,0,0,0) (1,0,0) (1,0,0)
>>> forceconstant 10.0
>>> }
>>> metadynamics {
>>> colvars cntdis
>>> hillWidth 2
>>> hillWeight 0.5
>>> newHillFrequency 100
>>> }
>>>
>>>
>>> Please let me know if someone has any insight regarding the same.
>>>
>>> Regards
>>> Sourav
>>>
>>
>>
>

-- 
Giacomo Fiorin
Assistant Professor of Research
Institute for Computational Molecular Science (ICMS)
College of Science and Technology, Temple University
1925 North 12th Street (035-07), Room 704D
Philadelphia, PA 19122-1801
Phone: +1-215-204-4213
Scholar: http://goo.gl/Q3TBQU
Personal: http://giacomofiorin.github.io/
Lab page: https://icms.cst.temple.edu/members.html
*"As computer programmers we have a responsibility to make sure that we run
the computers instead of the computers running us."*  - Steve Oualline

This archive was generated by hypermail 2.1.6 : Tue Dec 27 2016 - 23:22:10 CST