[gmx-users] R: R: help with neighborsearching error

Justin A. Lemkul jalemkul at vt.edu
Wed Feb 18 13:15:59 CET 2009

Anna Marabotti wrote:
> Dear Justin,
> just to answer to your comments: certainly I'm not expecting that things are going EXACTLY in the same way
> every time I repeat them, but it seems quite strange to me that the first time the system arrives to
> convergence and the next time not, with the same parameters...
> The other thing: when the system did not reach the Fmax requested, its potential energy was -3.66e+5, norm
> force was 1.31e+4 and the Fmax was 1621 (emtol was 1000). These values seem reasonable to me, am I wrong?

I have had problems with some of my systems any time Fmax > 1000.  Generally a 
range of 500-1000 seems reasonable, any more and you may experience problems.

> Anyway, I tried to minimize the system using emtol 500 and emstep 0.01 as you suggested (I enlarged it until 1
> previously, because from several trials it seemed to me that convergence was reached when timestep was
> larger). But probably the most important thing I found is that even in em.mdp file PME was not set (I really
> don't know why, probably I removed it unintentionally during some previous editing, without noticing it), so I
> added it and finally I reached convergence without errors. After then, the PR-MD worked without any problems.
> So it was really a stupid thing, and I'm sorry if I wasted your time, but without your help I would not have
> found this problem and fixed it.

Glad it worked!


> Thank you very much for your patience and help, and for your useful suggestions.
> Best regards
> Anna
> ______________________________________________
> Anna Marabotti, Ph.D.
> Laboratory of Bioinformatics and Computational Biology
> Institute of Food Science, CNR
> Via Roma 64
> 83100 Avellino (Italy)
> Phone: +39 0825 299651
> Fax: +39 0825 781585
> Skype: annam1972
> E-mail: amarabotti at isa.cnr.it
> Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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