[gmx-users] DPOSRES and energy minimization

[Justin Lemkul]

On 11/3/13 12:38 AM, Gianluca Interlandi wrote:
> Is it possible to use position restraints:
>
> define = -DPOSRES
>
> during an energy minimization? I tried to do that but it looks like all atoms
> are moved during minimization:
>

Depending on the forces present in the system, it is possible that the atoms 
will still move.  Position restraints do not prevent motion, they provide a 
biasing force that disfavors motion.  If the forces between your atoms are such 
that they overcome the bias, then indeed the atoms will move.

If you don't want them to move at all, then freeze them or use a stronger force 
constant for position restraints.  Doing so generally defeats the purpose of 
minimization, though.

-Justin

> ; VARIOUS PREPROCESSING OPTIONS =
> title                    =
> cpp                      = /lib/cpp
> include                  =
> define                   = -DPOSRES
>
> ; IMPLICIT SOLVENT OPTIONS =
> implicit-solvent         = GBSA
> gb-algorithm             = OBC
>
> ; RUN CONTROL PARAMETERS =
> integrator               = steep
> ; start time and timestep in ps =
> tinit                    = 0
> dt                       = 0.001
> nsteps                   = 1000
>
> ; ENERGY MINIMIZATION OPTIONS =
> emtol                    = 0.00001
> emstep                   = 0.01
> nstcgsteep               = 1000
>
> Thanks!
>
>       Gianluca
>
> -----------------------------------------------------
> Gianluca Interlandi, PhD gianluca at u.washington.edu
>                      +1 (206) 685 4435
>                      http://artemide.bioeng.washington.edu/
>
> Research Scientist at the Department of Bioengineering
> at the University of Washington, Seattle WA U.S.A.
> -----------------------------------------------------

-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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