Dear Justin thanks for your reply i trying to follow your tutorial but when i want to produce neccesary files per lambdas by this command: Perl write_mdp.pl em_steep.mdp i received 20 files as i expected but they are empty, for this reason i try to change some important parameters in your mdp file (we have mdp files for lambda=0) in other lambdas.for instance *init_lambda_state=0.05 or 0.1 or 0.15 , ...* but i dont know what value is instead of *delta_lambda?*
*mdp file for lambda=0* ; Free energy control stuff free_energy = yes **init_lambda_state = 0**delta_lambda = 0** calc_lambda_neighbors = 1 ; only immediate neighboring windows ; Vectors of lambda specified here ; Each combination is an index that is retrieved from init_lambda_state for each simulation ; init_lambda_state 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 vdw_lambdas = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00 also, you mentioned about *foreign_lambda* in your tutorial, but i didnot see it in mdp files. at the end, i want to know about the differences between *write_mdp.pl <http://write_mdp.pl>* and *write_sh.pl <http://write_sh.pl>* and* job.sh*? regards elham -- 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.
