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Removing fastest degrees of freedomTable of contentsNo headersWARNING -- This information has been culled from some gmx-users posts in October and November 2008. This information may be misleading or entirely inaccurate. In gromacs-4.0, Fatal error: Virtual site atom 29 is part of a charge group of only virtual sites, but its first constructing atom (26) is part of a different charge group, this combination is not allowed. This error message is also valid for older versions. It can not be guaranteed that the virtual sites in one charge group will have the same periodic shift. But before 4.0 there was no check for this. Using If you really want to use the One might try: dt = 0.004 constraints = all-bonds constraint_algorithm = lincs lincs-iter = 1 lincs-order = 6 Don't forget to change Using 5 fs without heavy hydrogens will not cause stability problems. It might cause slightly less accurate integration. But these integration errors are usually much smaller than other errors, such as cut-off errors. It is all a matter of what accuracy you want. If you want to be sure, you can run simulations with a 4 and 5 fs timestep (do not forget to modify In some users experience 5 fs works fine and they would not hesitate to use it for large systems, where one can anyhow not sample all conformational space. One user is currently mainly doing accurate calculations of thermodynamic quantities, for these they use 4 fs. |