[gmx-users] energy minimization - double precision
Dr Itamar Kass
ikass at uq.edu.au
Sat May 19 02:12:20 CEST 2007
When doing EM it is not a good idea to use restrains/constraints when
Try minimize without it.
"Prediction is very difficult, especially about the future" - Niels Bohr
| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
|Molecular Dynamics Group
| School of Molecular and Microbial Sciences (SMMS)
| Chemistry Building (#68)
| The University of Queensland
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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
> > followed by an mdrun, it does not converge even after 600 steps
> > returns saying that it could not get to the requested minimum
> > and suggested that i use double precision for the same. so, i
> > 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
> mdrun is a reasonable thing to try. Double precision minimization
> only something you care about before (say) a normal-mode analysis.
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