On 9/4/14, 9:42 PM, Lyna Luo wrote:
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!
Read the help description. The -ip (and all other similar input options) require a .dat file, which is a simple text file that lists the file names. You do not provide the actual file names themselves anywhere on the command line.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 [email protected] | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- 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].
