Dear All, I am doing umbrella sampling for a water molecules moving inside a crystal structure, however I am running into a problem on the output file with profile.xvg all value showing “nan”. This error has occurred when I reduce the slide width from 0.2 nm to 0.1 nm. I have used the exact pull code for 0.2 and 0.1, however only 0.2 has given me meaningful profile. The pull code I used is the following:
;Pull code pull = yes pull_ngroups = 2 pull_ncoords = 1 pull_group1_name = MOL pull_group2_name = SOL pull_coord1_type = umbrella ; harmonic biasing force pull_coord1_geometry = distance ; simple distance increase ;pull_coord1_vec = 0 0 1 pull_coord1_groups = 1 2 pull_coord1_dim = N N Y pull_coord1_rate = 0.01 ; 0.01 nm per ps = 10 nm per ns pull_coord1_k = 10 ; kJ mol^-1 nm^-2 pull_coord1_start = yes ; define initial COM distance > 0 and the time step I used is 500 ps, but I have also tried 100 and 50 ps. I have tried increasing the k value to 50 and 100 with the same results. The histogram shows many overlap, however when I use k value 100, it is only giving me individual single peak. Therefore can someone enlighten on what is going on? Best regards, Ben -- 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.
