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!
-Justin
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: amarabo...@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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--
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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