[gmx-users] Re: distance restraint

Justin Lemkul jalemkul at vt.edu
Fri Sep 28 18:21:04 CEST 2012

On 9/28/12 12:18 PM, pauladelgado wrote:
> The distance restraint energy is arrond 13700 KJ/mol, is that ok?, but whta
> happend with mi resulting pdb, i can't appreciate the distance restraint s i
> made.

No, that's not OK.  The very large value of energy suggests that the desired 
distances are not being achieved (which you can measure with g_dist).  How close 
are the initial distances to the restraints you have set in the topology?

> With respect to vacuum simulation, i am doing energy minimization and md
> with no periodic boundaries, with coulombtype=Cutt-off and the cut-offs turn
> off (equal to 0), and the md with no pressure and temperature cuopling, is
> that ok? Also i am not going to do NVT and NPT because for what i understand
> this is to equilibrate solvent and ions and make sure that this surround the
> protein.

The purpose of any ensemble is to obtain a conformational ensemble under those 
conditions.  What it sounds like you're trying to do is run an NVE simulation, 
which can be very difficult to obtain.  See the notes on the wiki for 
methodological issues.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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