[gmx-users] Re: Problems with cg
lindahl at stanford.edu
Thu Oct 17 19:16:55 CEST 2002
tccfr at ig.com.br wrote:
> Dear Erik,
> First of all I would like to thank you for your help in my last mail. It
>was very usefull.
> But now I am facing another problem, this time with minimization using cg.
>I have minimized one protein (DHFR) with steep until 201 Kj/mol.nm and now,
>I am trying to go on with cg. In my first round, I fixed a emtol of 200 just
>for testing. GROMACS stopped in step 1890 and output the following mesage:
>"Negative w: -2.828724731694e+17
> gpa = 2.656058552315e+08 gpb = 1,101866243368e+09
> a = 0,000000000000e+00, b = 1,404184966477e-08
> EpotA = -7.676745000000e+05,
>EpotB = -7.676685625000e+05 Negative number for sqrt encountered
> Terminating minimization
> Conjugate gradients did not converge in 10000 steps
> Function value at minimum = -7.6767e+05"
>This output put on me the questions:
>1) The value of Fmax at the moment of termination was 3.10116e+03. This
>value is smaller than the starting Fmax (201). How could it be possible ? Is
>that (3.10116e+03)a local minimum ? If so, how can I avoid it ?
We're actually minimizing the potential energy - the Fmax is just
information about the largest force on any atom in this conformation.
>2) What is w ?
>3) How can I avoid that w become negative ? or what should I do when this
You'll probably have to try double precision, or set nstcgsteep to e.g.
100 (perform a steepest descent step every 100 cg steps); there are a
couple of accuracy-sensitive operations in conjugate gradients, so
sometimes single isn't enough.
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