We've accomplished something similar by modifying the off-diagonal
Lennard-Jones terms (I might suggest changing the A coefficient while
keeping the B coefficient constant). You can do this with parmed. However,
depending on your current release of pmemd.cuda, such a prmtop may not work
just yet (I have the luxury/curse of having access to the developer tree,
so I can never tell what features are actually available to the "rabble").
Regards,
Brian
On Thu, Mar 27, 2014 at 12:03 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> 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/
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Mar 27 2014 - 10:00:03 PDT
