another thing to consider might be using negative force constants...
On Thu, Mar 27, 2014 at 11:34 AM, Thomas Evangelidis <tevang3.gmail.com>wrote:
> Dear AMBER list,
>
> I want to apply repulsive restraints between two ligands to prevent them
> from aggregating. I use the CUDA version 12.3 and hence I cannot apply
> forces to atom groups. Therefore I tried to adapt the typical parabolic
> well restraint to apply a repulsive force on a single atom of each ligand.
>
> &rst
> ialtd=0, ! the penalty energy continues to rise for large violations
> ir6=1, ! no center of mass averaging will be used
> iresid=0, ! IAT(I) points to an atom number (atom ID)
> iat=2855,2993, ! the distance between these two atoms will be used
> ! the restraint is a well with a square bottom with
> parabolic sides out to a defined distance, and then linear sides beyond
> that.
> ! If R is the value of the restraint in question:
> r1=0.0, ! R < r1 Linear, with the slope of the "left-hand" parabola
> at the point R=r1.
> r2=40.0, ! r1 <= R < r2 Parabolic, with restraint energy k2(R-r2)^2.
> r3=2000.0, ! r2 <= R < r3 E = 0
> r4=2500.0, ! r3 <= R < r4 Parabolic, with restraint energy
> k3(R-r3)^2.
> ! r4 <= R Linear, with the slope of the "right-hand"
> parabola at the point R=r4.
> rk2=20.0, ! force constant k2 (see above)
> rk3=20.0, ! force constant k3 (see above)
> &end
>
>
> Basically, I prevent attractive restraints between the ligands by setting
> r3 and r4 to very high values. However, I don't see any repulsion happening
> in the trajectory. Is my rationale correct? Is there any more effective and
> elegant way to apply repulsive restraints to the ligands?
>
> thanks in advance,
> Thomas
>
>
>
> --
>
> ======================================================================
>
> Thomas Evangelidis
>
> PhD student
> University of Athens
> Faculty of Pharmacy
> Department of Pharmaceutical Chemistry
> Panepistimioupoli-Zografou
> 157 71 Athens
> GREECE
>
> email: tevang.pharm.uoa.gr
>
> tevang3.gmail.com
>
>
> website: https://sites.google.com/site/thomasevangelidishomepage/
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Received on Thu Mar 27 2014 - 09:30:02 PDT
