Hello, I have created a consensus structure from the last ns of my trajectory using g_cluster with default parameters and -av for writing average structure. When I am trying to energy minimize output structure with steep I get a non-sense result -
Tolerance (Fmax) = 2.00000e+02 Number of steps = 3000 Step= 17, Dmax= 1.5e-06 nm, Epot= 1.51233e+18 Fmax= inf, atom= 11754 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 200 This problem does not occur when using g_cluster without -av averaging - minimization performs as usual with a conversion in about 1000 steps. Inspecting and comparing averaged and non-averaged structures I`ve found that 760 Leu (the one that is reported to have the highest energy) is corrupt - averaging creased the sidechain atoms to about two or three positions (I mean that several atoms overlap). Is that some kind of bug? Thanks. _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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
