[gmx-users] energy minimization - double precision

[Dr Itamar Kass]

Hi,

When doing EM it is not a good idea to use restrains/constraints when
doing EM.

Try minimize without it.

Best,
Itamar

---

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===========================================
| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
|
|Molecular Dynamics Group
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----- Original Message -----
From: Mark Abraham <Mark.Abraham at anu.edu.au>
Date: Friday, May 18, 2007 11:06 am
Subject: Re: [gmx-users] energy minimization - double precision
> 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.
> 
> Mark
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