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#7796 - 08/10/05 12:12 PM Is this possible in CHARMM (adding a routine) ?
cola Offline
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Registered: 07/28/04
Posts: 113
Dear All,

Let's assume that I have three atoms.
I'd like to get each position and
calculate the normal vector to a plane which is made by these three atoms.
(The normal vector will be changed during the simulation.)
Then, I'd like to apply a force to each atom along this normal vector.
Can I implement this kind of routine in a CHARMM code ?
Thank you in advance.


Edited by cola (08/10/05 01:31 PM)

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#7797 - 08/10/05 02:24 PM Re: Is this possible in CHARMM (adding a routine) ? [Re: cola]
rmv Online   content

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It depends on what you mean by "CHARMM code". I doubt that forces relative to a re-orienting vector can be done via a CHARMM script using available commands. I'm certain it could be done in the Fortran source. Some care might be required to make sure other aspects of the code aren't broken, such as energy conservation.
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#7798 - 08/10/05 04:11 PM Re: Is this possible in CHARMM (adding a routine) ? [Re: rmv]
cola Offline
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Registered: 07/28/04
Posts: 113
Thank you for your reply.
I meant whether it can be done within a CHARMM script.
I want to keep the applying force normal to the plane always during the simulation.
Do you mean that it is not possible to find the positions ( and the normal vector) because there is no such kind of command in CHARMM ?

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#7799 - 08/10/05 04:56 PM Re: Is this possible in CHARMM (adding a routine) ? [Re: cola]
rmv Online   content

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Correct, no existing command meets all of your requirements, esp. changing the direction of the applied force as the molecules rotates during dynamics.

The normal to a plane defined by a group of atom can be determined via

COOR LSQP NORM atom-selection

which will store the x,y,z components of the normal vector in the substitution values ?XAXI ?YAXI and ?ZAXI; see corman.doc

The PULL command (cons.doc) applies a force, but the vector orientation is fixed for the duration of the run.

Many of the commands in cons.doc are actually adding an applied force, but the vectors are typically based on atom coordinate positions in some way, as opposed to a derived vector (such as orthogonal to a plane formed by 3 atoms).
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Rick Venable
computational chemist


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#7800 - 08/10/05 07:01 PM Re: Is this possible in CHARMM (adding a routine) ? [Re: rmv]
cola Offline
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Registered: 07/28/04
Posts: 113
I'm a little confused.
If I know how to get the normal vector, then I think I can make a loop.

First, get a normal vector, and apply a force.
Then, after a few steps, get the normal vector again, and apply the force in a new direction.

Am I missing some points ?

Thank you in advance.

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#7801 - 08/10/05 09:28 PM Re: Is this possible in CHARMM (adding a routine) ? [Re: cola]
rmv Online   content

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It could be done that way, but saving trajectories would be complicated, and the overhead of restarting dynamics would be fairly inefficient; it would be much, much slower than regular MD.

You could probably run some "normal" dynamics first, and get the P2 correlation function of a unit vector between two of the atoms that will define the plane. The time decay could be used to gauge a reasonable estimate of how many dynamics steps you can do in the loop before the vector orientation changes too much.
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Rick Venable
computational chemist


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#7802 - 08/11/05 01:57 PM Re: Is this possible in CHARMM (adding a routine) ? [Re: rmv]
cola Offline
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Registered: 07/28/04
Posts: 113
I see.
Thank you for your suggestions.

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#7803 - 08/17/05 02:25 PM Re: Is this possible in CHARMM (adding a routine) ? [Re: rmv]
cola Offline
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Registered: 07/28/04
Posts: 113
Please let me ask you one more question.

I assume that there are two normal vectors on the plane (going up and going down).
Which one is saved in the XAXI, YAXI, and ZAXI ?

I mean, If I have 1,2, and 3 atoms, and make a normal vector using COOR LSQM NORM (1,2,3 atoms), then the direction of normal vector is given by the clockwise or counter-clockwise rotation ?

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#7804 - 08/17/05 02:42 PM Re: Is this possible in CHARMM (adding a routine) ? [Re: cola]
rmv Online   content

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Registered: 09/17/03
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It may be arbitrary, dependent on the numerical solution to the best fit plane; I'm not aware of any way to enforce a "right hand rule" based on the order of selected atoms or anything like that. You may have to test the vector and invert it if it points the wrong way.
_________________________
Rick Venable
computational chemist


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#7805 - 08/17/05 05:31 PM Re: Is this possible in CHARMM (adding a routine) ? [Re: rmv]
cola Offline
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Registered: 07/28/04
Posts: 113
Thank you so much.
I'll check this.

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