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

Anna Marabotti anna.marabotti at isa.cnr.it
Wed Feb 18 12:06:02 CET 2009

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?

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.
Thank you very much for your patience and help, and for your useful suggestions.
Best regards

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
"If you think you are too small to make a difference, try sleeping with a mosquito"

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