Dear gmx experts, I'm using g_wham version 5.0 to generate PMF from non-gromacs umbrella sampling. Following the option -ip, I prepared all pdo files in one directory and gzip them. Then I run "g_wham -v -ip *.gz -bins 400 -temp 300 -tol 0.00001 -auto". The output shows:
GROMACS: gmx wham, VERSION 5.0 Executable: /usr/local/gromacs/bin/gmx Library dir: /usr/local/gromacs/share/gromacs/top Command line: g_wham -v -ip job.job13.0.sort.colvars.traj,temp.pdo.gz job.job13.10.sort.colvars.traj,temp.pdo.gz job.job13.11.sort.colvars.traj,temp.pdo.gz job.job13.12.sort.colvars.traj,temp.pdo.gz job.job13.13.sort.colvars.traj,temp.pdo.gz job.job13.14.sort.colvars.traj,temp.pdo.gz job.job13.15.sort.colvars.traj,temp.pdo.gz job.job13.16.sort.colvars.traj,temp.pdo.gz job.job13.17.sort.colvars.traj,temp.pdo.gz job.job13.18.sort.colvars.traj,temp.pdo.gz job.job13.19.sort.colvars.traj,temp.pdo.gz job.job13.1.sort.colvars.traj,temp.pdo.gz job.job13.61.sort.colvars.traj,temp.pdo.gz job.job13.62.sort.colvars.traj,temp.pdo.gz job.job13.63.sort.colvars.traj,temp.pdo.gz job.job13.6.sort.colvars.traj,temp.pdo.gz job.job13.7.sort.colvars.traj,temp.pdo.gz job.job13.8.sort.colvars.traj,temp.pdo.gz job.job13.9.sort.colvars.traj,temp.pdo.gz -bins 400 -temp 300 -tol 0.00001 -auto ------------------------------------------------------- Program g_wham, VERSION 5.0 Source code file: /root/gromacs-5.0/src/gromacs/commandline/pargs.cpp, line: 874 Invalid command line argument: job.job13.10.sort.colvars.traj,temp.pdo.gz For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors If I run single pdo file, it shows different error message: Command line: g_wham -v -ip job.job13.0.sort.colvars.traj,temp.pdo.gz -bins 400 -temp 300 -tol 0.00001 -auto ------------------------------------------------------- Program g_wham, VERSION 5.0 Source code file: /root/gromacs-5.0/src/gromacs/fileio/futil.cpp, line: 540 File input/output error: job.job13.0.sort.colvars.traj,temp.pdo.dat My pdo file format is: # UMBRELLA 3.0 # Component selection: 0 0 1 # nSkip 1 # Ref. Group TestAtom # Nr. of pull groups 1 # Group 1 GR1 Umb. Pos. 0 Umb. Cons. 2.0 ##### 5054910 6.86778783227709e-01 5054920 7.12201410957491e-01 5054930 7.20695103841784e-01 5054940 7.10706445794138e-01 5054950 7.30693655979543e-01 5054960 7.33930839499955e-01 5054970 7.45784725425651e-01 5054980 7.66841219351832e-01 5054990 7.61835548305989e-01 5055000 7.69643361420997e-01 Is my pdo file format right? What is the correct way to use g_wham -ip option? Thank you! Lyna -- 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 [email protected].
