Dear All, As I have specified in my earlier mail, I wanted to know which input trajectory has to be supplied to -rerun flag in mdrun for recalculation of electrostatic energies between protein-solvent from gromacs (as proposed by Lindgren et al, in the paper "On the stability of chymotrypsin inhibitor 2 in a 10 M urea solution. The role of interaction energies for urea-induced protein denaturation",) <http://pubs.rsc.org/en/content/articlehtml/2010/cp/b925726h>.
As I was confused about the input files, I am doing a trial where I am supplying the production run trajectory to -rerun. This involves making changes in the cut-offs and applying cut-off scheme rather than PME. My cubic box length is 3.20 and I cannot specify any cutoffs exceeding half of this length,(without changing the box length). So I apply whatever cut-offs are possible with my present box size. I am getting the error: *Rerun trajectory frame step 0 time 0.000000 has too small box dimensions* after running mdrun Please help me troubleshoot the issue Thanking you, Yours sincerely, Apramita Chand -- 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.
