[gmx-users] Normal Mode Analysis in Double-Precision

Ran Friedman r.friedman at bioc.uzh.ch
Thu Jul 31 14:14:38 CEST 2008


It's hard to know why you get a segmentation fault without further info.
Did you ran the GMX tests after installation with double precision? Is
everything all right there?

Also, when exactly the system crashes? Is it straight when you start
mdrun? Did you use both grompp and mdrun in double precision?

Good luck,

Inon Sharony wrote:
> Hi all!
> I'm trying to perform a normal mode (NM) analysis, but having trouble
> with the
> recommendation of first performing a double precision energy
> minimization before writing
> the Hessian. The calculation of the Hessian matrix is done using
> mdrun, and its
> diagonalization is done using g_nmeig. I have managed this procedure
> using single-precision, but if the recommended maximal force (the
> minimization convergence criterion) is 1E-5 kJ mole^-1 nm^-1 , I was
> only able so far to get to 1E-2 before getting a message that the
> minimization algorithm has reached machine precision. I have tried
> Conjugate Gradient and L-BFGS.
> I also compiled GROMACS in double-precision, but for some reason when
> I try to minimize the energy of the same molecules, I get a
> segmentation fault. I'm not sure where this is coming from (already
> checked the user lists).
> Can someone with experience in Normal Mode analysis in GROMACS (or
> just general
> experience in using GROMACS with double-precision) help me with my
> difficulty?
> (Currently I'm running pentane or para-dimethylbenzene)
> Thanks for your help,
> --Inon   Sharony
> ×™× ×•×Ÿ     ×©×¨×•× ×™
> +972(3)6407634
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Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-6355593
Email: r.friedman at bioc.unizh.ch
Skype: ran.friedman

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