**From:** Jérôme Hénin (*jerome.henin_at_ibpc.fr*)

**Date:** Fri Sep 01 2017 - 10:48:49 CDT

**Next message:**Ben Adams: "Re: problem with minimization and calculation of force on a fixed atom"**Previous message:**Ben Adams: "Re: problem with minimization and calculation of force on a fixed atom"**In reply to:**Ben Adams: "Re: problem with minimization and calculation of force on a fixed atom"**Next in thread:**Ben Adams: "Re: problem with minimization and calculation of force on a fixed atom"**Reply:**Ben Adams: "Re: problem with minimization and calculation of force on a fixed atom"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Indeed... What I suspect might be happening here is that the constraint

force gets included in the reported total force, which adds up to zero.

Jerome

On 1 September 2017 at 17:36, Ben Adams <benny.adams1993_at_gmail.com> wrote:

*>
*

*> Thanks but even when I use fixedAtomsForces it still returns zeros. For
*

*> example here atom 2431 is frozen but the force output is zeros:
*

*>
*

*>
*

*> fixedAtoms on
*

*>
*

*> fixedAtomsForces on
*

*>
*

*> fixedAtomsFile fix.pdb
*

*>
*

*> fixedAtomsCol B
*

*>
*

*> tclForces on
*

*>
*

*> tclForcesScript {
*

*>
*

*>
*

*> set nter [addgroup {1}]
*

*>
*

*> set cter [addgroup {2431}]
*

*>
*

*> proc calcforces {} {
*

*>
*

*> global cter
*

*>
*

*> loadcoords coor
*

*>
*

*> enabletotalforces
*

*>
*

*> if {[getstep] > 0} {
*

*>
*

*> loadtotalforces forces
*

*>
*

*> print $forces($nter)
*

*>
*

*> # print cter= $forces(cter)
*

*>
*

*> }
*

*>
*

*> }
*

*>
*

*> }
*

*>
*

*> On Thu, Aug 31, 2017 at 5:36 PM, Jérôme Hénin <jerome.henin_at_ibpc.fr>
*

*> wrote:
*

*>
*

*>> I've been told of a certain command named fixedAtomsForces that sounds
*

*>> just like what you need :-)
*

*>>
*

*>> Jerome
*

*>>
*

*>> On 1 September 2017 at 00:03, Ben Adams <benny.adams1993_at_gmail.com>
*

*>> wrote:
*

*>>
*

*>>> Dear NAMD users,
*

*>>>
*

*>>> I want to calculate forces on a few constrained atoms while I'm doing
*

*>>> merely energy minimization. I used colvars with harmonic restraints and
*

*>>> obtained force based on the distance of the atom of interest to a specified
*

*>>> Center value. But the minimization causes dramatic fluctuations on
*

*>>> calculation of force. Changing the force constant, minimization options
*

*>>> mentioned in tutorial don't help that much. and the results are not even
*

*>>> reproducible.
*

*>>> An alternative way would be to freeze that atom and calculate the force
*

*>>> directly. But using the 'fixedAtoms' option leaves the force at the atom
*

*>>> equal to zero and do not allow to extract its value.
*

*>>> Is there any other way to freeze an atom while the force on it is being
*

*>>> calculated?
*

*>>> Or is there anyway to make minimization more stable when a colvar
*

*>>> constraint is present?
*

*>>>
*

*>>> Thanks in advance,
*

*>>>
*

*>>>
*

*>>>
*

*>>
*

**Next message:**Ben Adams: "Re: problem with minimization and calculation of force on a fixed atom"**Previous message:**Ben Adams: "Re: problem with minimization and calculation of force on a fixed atom"**In reply to:**Ben Adams: "Re: problem with minimization and calculation of force on a fixed atom"**Next in thread:**Ben Adams: "Re: problem with minimization and calculation of force on a fixed atom"**Reply:**Ben Adams: "Re: problem with minimization and calculation of force on a fixed atom"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

*
This archive was generated by hypermail 2.1.6
: Mon Dec 31 2018 - 23:20:34 CST
*