**From:** Yun Luo (*luoyun724_at_gmail.com*)

**Date:** Thu Oct 13 2011 - 09:03:46 CDT

**Next message:**Yun Luo: "Re: Boundary potential of colvar alpha not working?"**Previous message:**francesco oteri: "Re: iron sulphur cluster parametrization"**In reply to:**Jérôme Hénin: "Re: Boundary potential of colvar alpha not working?"**Next in thread:**Jérôme Hénin: "Re: Boundary potential of colvar alpha not working?"**Reply:**Jérôme Hénin: "Re: Boundary potential of colvar alpha not working?"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Hi Jerome,

Maybe I asked too many questions at the same time. Sorry about the rush. My first question is: if the wallpotential can be applied to colvar alpha without turning on the extendedLagrangian? Because in ug, it says "System forces are available currently only for the following components: distance, distanceZ, distanceXY, angle, dihedral, rmsd, eigenvector and gyration." . The colvars alpha is not included in calculating system forces.

Thanks!

Lyna

On Oct 13, 2011, at 8:54 AM, Jérôme Hénin wrote:

*> Hi Lyna,
*

*>
*

*> I can't say anything more specific unless you tell me roughly what you
*

*> are trying to achieve.
*

*>
*

*> Jerome
*

*>
*

*> On 13 October 2011 15:21, Yun Luo <luoyun724_at_gmail.com> wrote:
*

*>> Thanks Jerome! I think I tried the wall potential constant until 1000. But I can try with even higher constant (Is it a quadratic harmonic potential?) But what about the extendedLagrangian force constant? Does it necessary ? If yes, how to balance to wall force constant with extendedlagrangian force constant?
*

*>>
*

*>> Thanks!
*

*>>
*

*>> Lyna
*

*>>
*

*>> On Oct 13, 2011, at 7:14 AM, Jérôme Hénin wrote:
*

*>>
*

*>>> Hi Lyna,
*

*>>>
*

*>>> The "wall" potentials are actually soft, so the colvar is not strictly
*

*>>> constrained to be inside the range. In particular, if the colvar is
*

*>>> subject to high forces, the bias is not always enough to overcome
*

*>>> them. This could be the case here. Since the full range of the
*

*>>> coordinate is [0, 1], a force constant of 100 is not huge. You could
*

*>>> try a higher value.
*

*>>>
*

*>>> Cheers,
*

*>>> Jerome
*

*>>>
*

*>>>
*

*>>> 2011/10/12 Yun Luo <luoyun724_at_gmail.com>:
*

*>>>>
*

*>>>> Dear NAMD supporter,
*

*>>>>
*

*>>>> I'm using "alpha" colvar for a deca-alanine peptide in vacuum. I set up the boundary for alpha 0.0 to 2.5 as below. And I increased the wallconstant and decrease the extendedFluctuation as below. However, during 2 ns the configuration just stays stable at the region outside of by alpha boundary. It seems to me that no matter what constant I use, the boundary potential is not working for alpha colvar, no matter extendedLagrangian is turned on or off. I tested with distance colvar, the boundary potential works well though.
*

*>>>> The outputAppliedForce is fluctuating between -2000 and 2000, but average around 0.
*

*>>>> The outputSystemForce is 0.
*

*>>>> The MISC in NAMD's energy output is fluctuating between 0 and 5, but average around 1.
*

*>>>> The Boundary in NAMD's energy output is 0.
*

*>>>>
*

*>>>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*

*>>>>
*

*>>>> colvarsTrajFrequency 100
*

*>>>> colvarsRestartFrequency 100000
*

*>>>>
*

*>>>> colvar {
*

*>>>> name alpha
*

*>>>> width 0.01
*

*>>>> lowerboundary 0.0
*

*>>>> upperboundary 0.25
*

*>>>> lowerwallconstant 100.0
*

*>>>> upperwallconstant 100.0
*

*>>>> extendedLagrangian on
*

*>>>> extendedFluctuation 0.0005
*

*>>>> outputValue on
*

*>>>> outputVelocity on
*

*>>>> outputEnergy on
*

*>>>> outputSystemForce on
*

*>>>> outputAppliedForce on
*

*>>>>
*

*>>>> alpha {
*

*>>>> residuerange 1-10
*

*>>>> psfSegID HLX
*

*>>>> hbondcoeff 0.5
*

*>>>> angleref 88
*

*>>>> angletol 15
*

*>>>> hbondcutoff 3.3
*

*>>>> hbondexpnumer 6
*

*>>>> hbondexpdenom 8
*

*>>>> }
*

*>>>> }
*

*>>>>
*

*>>>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*

*>>>>
*

*>>>> Thanks a lot!
*

*>>>>
*

*>>>> Lyna
*

*>>>>
*

*>>>>
*

*>>
*

*>>
*

**Next message:**Yun Luo: "Re: Boundary potential of colvar alpha not working?"**Previous message:**francesco oteri: "Re: iron sulphur cluster parametrization"**In reply to:**Jérôme Hénin: "Re: Boundary potential of colvar alpha not working?"**Next in thread:**Jérôme Hénin: "Re: Boundary potential of colvar alpha not working?"**Reply:**Jérôme Hénin: "Re: Boundary potential of colvar alpha not working?"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

*
This archive was generated by hypermail 2.1.6
: Wed Feb 29 2012 - 15:57:49 CST
*