RE: Component distanceZ-ABF

From: Parisa Akhski (Parisa.Akhshi_at_chem.queensu.ca)
Date: Mon Sep 05 2011 - 09:42:17 CDT

Hi Jerome,

I think I know what is going on now. I only have one question:

If I use a dummy atom to define the "ref" and move the ion "main" along e( 1 0 0), what does the sign of force mean? If force is positive, does this mean the ion tends to move away from ref?

Thanks,

Parisa

-----Original Message-----
From: heninj_at_gmail.com on behalf of Jérôme Hénin
Sent: Fri 9/2/2011 5:19 PM
To: Parisa Akhski
Cc: namd-l_at_ks.uiuc.edu
Subject: Re: namd-l: Component distanceZ-ABF
 
Hi Parisa,

Did you check the DCD trajectory (in VMD) or the colvars.traj file? I
recommend looking at both and checking that the value seen by the
colvars module is the one you expect based on the atomic coordinates.

Jerome

On 2 September 2011 18:21, Parisa Akhski <Parisa.Akhshi_at_chem.queensu.ca> wrote:
>
> Dear NAMD experts,
>
> I want to move an ion (atomnumbers {1}) along an axis (X axis) while my
> channel is along Z. I am using "Component distanceZ" as mentioned in NAMD
> 2.7b3 to do so.
>
>
> lowerboundary 0.0
> upperboundary 4.0
>
> lowerwallconstant 100.0
> upperwallconstant 100.0
>
> distanceZ {
> main {
> atomnumbers { 1 }
> }
> ref {
> atomnumbers { 2 3 4 5 }
> }
> axis (1.0, 0.0, 0.0)
> }
>
> To my understanding, this should change the value of the component e·(r -
> r1) from 0 to 4 along X. Also to confine the ion movement along Y and Z, I
> defined another colvar as below:
>
> lowerboundary -0.1
> upperboundary 0.1
>
> lowerwallconstant 100.0
> upperwallconstant 100.0
>
> distanceXY {
> main {
> atomnumbers { 1 }
> }
> ref {
> atomnumbers { 2 3 4 5 }
> }
> axis (1.0, 0.0, 0.0)
> }
>
> I believe this should confine the ion movement in the a plane orthogonal to
> the X axis (1.0, 0.0, 0.0) defined by the first colvar. However, by checking
> the trajectory file for the ion positions, it seems that the ion is not
> moving properly in any of the directions. It's position has changed by 2A
> along Z right after starting the simulation and fluctuates within 2-3A
> during the simulation. Along Y, it fluctuates within 1.5A and along X
> although it is supposed to move within only 4A, it experiences a much wider
> range (8A). I am wondering whether I misunderstood something in the commands
> above.
>
> Many thanks,
>
> Parisa
>

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