Re: constraintScaling - FOR LOOP

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Fri May 30 2008 - 08:30:07 CDT

Hi Samuel,
this should work fine; you should also be able to verify the effects by
switching the constraintScaling to 0 and checking that the appropriate
column of the energy output drops to 0.
Peter

Semorale wrote:
> Dear NAMD`users:
>
> I need to gradually reduce constrainst with constraintScaling, and for
> this, I have the next for loop:
>
> for {set a 9} {$a > 2} {incr a -1} {
> set b [expr {double($a)/10}]
> constraintScaling $b
> run 50
>
> According to the user manual for NAMD
> (http://www.ks.uiuc.edu/Research/namd/2.6/ug/node28.html),
> constraintScaling, works only if constraints are active. The point is
> that even with the constraints deactivated, anyway works the for
> loop,hence, I think that this is not the decreasing constraints , but
> just doing a MD loop. My .namd file is:
>
> if {1} {
> constraints on
> consRef restrain_BB.pdb
> consKFile restrain_BB.pdb
> consKCol B
> }
>
> If this does not work, and I in separately job, decrease the constraint,
> Does each time that finish a job, I have to make a new constraints
> file to .coor a work previous?
>
>
>
> Could you help me with this?. Any suggestion to me is useful
>
> Samuel

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