[gmx-users] successive removal of position restrain?

[Justin Lemkul]

On 9/6/17 5:36 AM, Seera Suryanarayana wrote:
> Dear gromacs users,
> 
> I have gone through one gromacs tutorial of md simulation in solvent. Where
> they mentioned that successive removal of position restrain. In other words
> first they have done NPT ensemble with 1000  1000  1000 energy constants,
> then re executed the NPT ensemble with 100   100   100 energy constants and
> finally third time they ran the NPT ensemble with 10   10   10 energy
> constants. After this run they have stated the real MD production run with
> position restraint. But I have done NPT ensemble only with 1000  1000 1000
> force constant and then I removed the complete position restrains before MD
> production run. My question comes here, Is there any difference between
> their methodology and my methodology?
> 

Well, naturally there is a difference, but whether or not it matters is a 
different question :)

I have never done step-wise removal of position restraints.  Some people swear 
by it.  Same story with warming a system from 0 K to a target temperature - I 
see no benefit but others believe it's necessary.  The purpose of equilibration 
is to relax the system and achieve a reasonably stable thermodynamic ensemble. 
If you've done that, proceed with your simulation.

-Justin

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Justin A. Lemkul, Ph.D.
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Virginia Tech Department of Biochemistry

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