Hello all, My simulation involves the pulling of a protein in the negative direction of the z-axis into a stationary hydrophobic self-assembled monolayer surface model (MTHL) using the position pull geometry. My umbrella parameters in the md_umbrella.mdp file are as follows:
pull = umbrella pull_geometry = position pull_vec1 = 0 0 1 pull_start = yes pull_ngroups = 1 pull_group0 = MTHL pull_group1 = Protein ;pull_init1 = 0 pull_rate1 = 0.0 pull_k1 = 500 My output pullf files have three dimensions in them because of the pull_vec definition, so I wrote a script to calculate the magnitude of the pull force and to return the files with a time column and a force column. I was told by g_wham to make my own pdo files, but am struggling to do so; it looks like I have to insert a header with all the umbrella information for each run in the beginning of each file. I believe the header for my files should look like this: # UMBRELLA 3.0 # Component selection: 0 0 1 # nSkip 1 # Ref. Group ’MTHL’ # Nr. of pull groups 1 # Group 1 'Protein’ Umb. Pos. Z Umb. Cons. 500 ##### I'm not sure what nSkip means and I'm not sure what I should put for Component selection. Can someone give me a quick tutorial or a script that helps create pdo files? I tried passing the files I created with the force magnitudes to g_wham as normal pullf files (since those don't have strange headers); however, using the -if option requires the -it option and those tpr files contain information about the pull_vec that generates this output: Fatal error: Found pull geometry 'position' and more than 1 pull dimension (3). Hence, the pull potential does not correspond to a one-dimensional umbrella potential. Is there a simpler way to do g_wham with position pull geometry? I believe my intuition to calculate the magnitude of the force is correct but would be interested to see if anyone thinks only the z-component of the umbrella force is of interest. Thanks, David Peeler Matysiak Biomolecular Modeling Laboratory Fischell Department of Bioengineering University of Maryland, College Park -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
