Hi, thanks for your response, Since I'm using pull_geometry=position I was under the impression that defining pull_dim was not necessary. Instead, I defined pull_vec to specify that the protein should be pulled along <0 0 1> I was previously using pull_geometry=distance with pull_dim= N N Y but found that at slow pull_rates the protein actually moved in the opposite direction that I wanted. I am using a negative pull_k but from what I've read that is fine. I will try to use pull_dim along with the pull_vec definition while using pull_geometry=position, I just thought the two were mutually exclusive.
Thanks, David On Tue, Nov 6, 2012 at 8:08 AM, Jochen Hub <j...@gwdg.de> wrote: > Hi, > > are you sure that you want to have pull_dim = Y Y Y (which is the > default)? When you want to pull only in z direction, I would use pull_dim = > N N Y. Otherwise, your z coordinate is not your reaction coordinate. > > If you want to pull in 3 dimensions you probably want to use > pull_geomery=distance. > > Hope this helps, > Jochen > > > Am 11/4/12 7:17 PM, schrieb David Peeler: > > 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 >> >> > -- > ------------------------------**--------------------- > Dr. Jochen Hub > Computational Molecular Biophysics Group > Institute for Microbiology and Genetics > Georg-August-University of Göttingen > Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. > Phone: +49-551-39-14189 > http://cmb.bio.uni-goettingen.**de/ <http://cmb.bio.uni-goettingen.de/> > ------------------------------**--------------------- > -- David Peeler <http://www.linkedin.com/pub/david-peeler/3b/b4b/123> President,* *Society of Biological Engineers University of Maryland, College Park '13 -- 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
