[gmx-users] DPOSRES and energy minimization

[Gianluca Interlandi]

Is there a way to tell from the log file whether positional restraints are 
really activated or not?

Thanks,

      Gianluca

On Sun, 3 Nov 2013, Justin Lemkul wrote:

>
>
> 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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-----------------------------------------------------
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.
-----------------------------------------------------