Dear Users, I have encountered several questions when I try to perform NMA on a protein structure from an equilibrated MD simulation. I were basically referred to the gromacs manual ( http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis) and some threads in the mailing list.
First, Gromacs (and in some literature) suggest to have L-BFGS energy minimization (sometimes after steep and cg calculations) of the structure before NMA and L-BFGS generally requires shifted/switched interactions. However, for vdW the option should have been changed by introducing the vdw-modifier and l-bfgs seems to still recognize it as cutoff. Second, for electrostatics, the option has been improved by Reaction-field-zero but is it still suitable for NMA calculation? Third, I have achieved a maximum force of 9.78750e-01 using cg and still got the warning: "The force is probably not small enough to ensure that you are at a minimum." Usually how stable do we have to achieve in order to avoid the warning? Thanks in advance for any experience shared. Kevin OSU Pharmacy -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.