[gmx-users] energy minimization - double precision

Mark Abraham Mark.Abraham at anu.edu.au
Fri May 18 05:06:29 CEST 2007

Pradeep Kota wrote:
> Dear users,
> I'm trying to minimize the energy of a protein in vacuum. I have 
> restrained the backbone with posre.itp generated using genpr. when i try 
> to minimize the energy of this protein using single precision grompp 
> followed by an mdrun, it does not converge even after 600 steps and 
> returns saying that it could not get to the requested minimum energy, 
> and suggested that i use double precision for the same. so, i compiled 
> gromacs with double precision and tried the same and i get the 
> following. Could you help me solve this?

Try a visual inspection of your structure before and after the 
single-precision minimization and look for sources of problems. You 
don't actually need convergence of minimization before an equilibration 
mdrun is a reasonable thing to try. Double precision minimization is 
only something you care about before (say) a normal-mode analysis.


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