From: Jérôme Hénin (jerome.henin_at_uhp-nancy.fr)
Date: Tue Nov 02 2004 - 18:24:07 CST
Hi Ben,
I don't understand what you're trying to do with angle units in your code:
---------------
set phi [getdihedral $p($atoms1($j)) $p($atoms2($j)) $p($atoms3($j))
$p($atoms4($j))]
# phi is in degrees, between -180 and +180
set phi [expr $phi*$pi/180]
# now it's radians, between -pi and +pi
addenergy [expr $k*($phi-180)*($phi-180)/2]
set force [expr -$k*($phi-180)]
# looks like you actually want degrees there
---------------
...which means that you are constantly applying a force of about (180-pi)*k on
your dihedral.
Best,
Jerome
Le mercredi 3 Novembre 2004 00:01, Ben Roberts a écrit :
> Hi all,
>
> Recently I have been trying to use Tcl dihedral restraints during a
> minimisation to force amides to go trans.
>
> This seems to badly break the conjugate gradients algorithm, whether
> "addenergy" is turned on or off. The energy, even, seems to maximise
> rather than minimise.
>
> Does anyone have any idea why this should be the case?
>
> Attached is my Tcl script (restraints.tcl) for your information.
>
> Thanks in advance, and best regards,
>
> Ben
>
> ----------------------------------------------------------------------
> Benjamin P. Roberts, B.Sc.(Hons)
> Ph.D. Student
>
> Department of Medicinal Chemistry
> Victorian College of Pharmacy (Monash University)
> 381 Royal Parade, Parkville VIC 3052, Australia
>
> Phone +61 3 9903 9674 | Fax +61 3 9903 9582 | Mobile +61 401 784 940
> ----------------------------------------------------------------------
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