**From:** Giacomo Fiorin (*giacomo.fiorin_at_gmail.com*)

**Date:** Tue Mar 27 2012 - 21:13:00 CDT

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Hello Chang, the extreme values depend on the way you computed the vector

that you're providing.

Say that you computed the vector V as the difference between two structures

A and B, and you normalized it so that |V| = 1, and chose A as the

reference structure. If we call C the simulated structure, the value is (C

- A) * V. It will give you 0 if C is near A, and 1 if C is near B. Mind

that there is also a correction because V gets centered around zero by the

code, so in this particular example the actual range is -0.5 to 0.5. If

|V| is different from one, you can do the conversion easily.

If you're in doubt, try setting up a test calculation using A as reference

coordinates, and one using B as reference coordinates. The two values of

the eigenvector colvar should give you a good estimate of the actual range

of values.

Giacomo

On Tue, Mar 27, 2012 at 8:46 PM, chang <chang.luchang_at_gmail.com> wrote:

*> Dear Sir/Madam,
*

*>
*

*> I have been trying to use eigenvector as the coordinate of ABF simulation
*

*> (to sample the space between a starting molecule and an ending molecule).
*

*> But I have trouble on deciding the upperWall/lowerWall and the force:
*

*> upperWallConstant/**lowerWallConstant. Information in the user's guide is
*

*> far from enough. Could you give me some suggestion on choosing these
*

*> parameters?
*

*>
*

*> (BTW. The molecule in question has approximately 4800 atoms and 66000
*

*> atoms underwater. )
*

*>
*

*> Your answer would be greatly appreciated.
*

*>
*

*> Best regards,
*

*> Chang Lu
*

*>
*

*>
*

**Next message:**Norman Geist: "AW: How to Get Bonded Pair Force Calculation with NAMD"**Previous message:**Chris Harrison: "Re: 2.9b1 crashes"**In reply to:**chang: "collective variable component -- eigenvector usage"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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