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

[Anna Marabotti]

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

______________________________________________
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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