[gmx-users] Position restraints

[Justin A. Lemkul]

Mikhail Stukan wrote:
> Dear gmx-users,
> 
>  
> 
> I am trying to simulate a thermalized wall in the framework of CG 
> Martini force field. To do this I am planning to link my wall atoms to 
> some reference points (initial positions) by harmonic potentials. From 
> what I have found in the manual it looks like this can be done by using 
> [position_restraints] declaration. What is not clear to me from the 
> manual is if I understand correctly that as the “reference position” 
> GROMACS will use the initial positions of the particles mentioned in 
> [position_restraints] decraration? If yes then which positions of the 

Correct.

> wall particles will be written out at the end of the run? The initial 
> ones (“reference positions”) or the instantaneous position of these 
> particle at the end of the run?
> 
>  

The instantaneous positions.  Since the atoms can move using position restraints 
(with the amount controlled by the force constant specified), there is no 
guarantee that the positions will not change, and in fact, they usually do, even 
if the amount is very small.

-Justin

> 
> Many thanks in advance,
> 
> Mikhail
> 
>  
> 
> =============================================
> 
> Dr Mikhail Stukan
> 
> Schlumberger Dhahran Carbonate Research Center,
> 
> Dhahran Techno Valley  - KFUPM,
> 
> P.O. Box 39011, Dammam / Doha Camp  31942,
> 
> Kingdom of Saudi Arabia
> 
> Tel: +966 3 331 6182
> 
> Fax:+966 3 330 0845
> mstukan at slb.com <mailto:mstukan at slb.com>
> 
>  
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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