Greetings All; I have reinstalled my Rocks cluster which went from CentOs4 to CentOs5 . I downloaded the Gromacs 3.3.2 RPMs, and although the examples work fine, my own simulations (surface tethered species, OPLS-AA) are blowing up, even though they are minimized as usual. I see no differences in the topologies, but the blow-up clearly starts near the tether points. I went back to a tpr file that worked well previously with v3.3, but even it diverges with the LINCs constraint failures after 10-50 ps, depending on the run.
If all of the run information is in the tpr file, does this mean that the mdrun codes are significantly different? Should I expect to have similar levels of stability under different versions of gromacs? Are Gromacs v4 RPMs available? I did not see them on the website ... I thank you in advance for your help Cheers! Prof. Paul Rowntree Dept. of Chemistry, University of Guelph
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