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: [email protected] 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" _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
