[gmx-users] pull code problem: between protofilaments
Dear Shilpi: Can you use something like this? pull = umbrella pull_geometry= position pull_dim = N N Y pull_vec1= 0 0 0 pull_start = no pull_ngroups = 1 pull_group0 = PRO-1 pull_pbcatom0= pull_group1 = PRO-2 pull_pbcatom1= pull_init1 = 0 0 pull_rate1 = 0 pull_k1 = 500.0 pull_nstxout = 500 pull_nstfout = 500 The above is for umbrella sampling. If you want to do continuous pulling, then: pull_start = yes pull_rate1 = ### Also: Next time you post, please provide more specifics. For example, I suggested a .mdp file in specifics to you above and I bet it would have been harder for you to guess what I meant if I had just told you the general idea instead of pasting some .mdp options. Likewise, your initial post would have been clearer it you had copied and pasted the .mdp pull code section that you tried to use. Chris. -- original message -- Dear Gmx users, I am studying the interaction between the tubulin protofilaments arranged in parallel. For this operation, I have considered a tetramer and a dimer from two protofilaments respectively (say PRO-1 and PRO-2), tetramer in PRO-1 and a dimer in PRO-2. I want to move the dimer of PRO-2 over the tetramer of PRO-1 along the length of protofilaments in one axis only, keeping the PRO-1 fixed to its original position. I tried by assuming tetramer as 'reference group' and the dimer as 'pull group' in pull code but the system crashed. I have succeeded in separating two dimers in Z-axis by using 'distance' geometry. But this case is quite different, as the pulling is not face-to-face but rather a sliding movement over another protofilament. Here, the COM distance between the pull group (dimer of PRO-2) and reference group (tetramer of PRO-1) first decreases and then increases while it moves. How can I simulate this operation by using pull code? Thanks, best regards, Shilpi Chaurasia -- gmx-users mailing listgmx-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
[gmx-users] Adjust the screen's output frequency
How to change the screen's output frequency? ol 0.85 imb F 6% step 4188000, remaining runtime: 174 s vol 0.87 imb F 3% step 4188100, remaining runtime: 174 s vol 0.86 imb F 1% step 4188200, remaining runtime: 174 s vol 0.86 imb F 4% step 4188300, remaining runtime: 174 s vol 0.88 imb F 6% step 4188400, remaining runtime: 174 s vol 0.87 imb F 3% step 4188500, remaining runtime: 174 s vol 0.88 imb F 8% step 4188600, remaining runtime: 174 s vol 0.88 imb F 6% step 4188700, remaining runtime: 174 s vol 0.86 imb F 3% step 4188800, remaining runtime: 174 s vol 0.87 imb F 4% step 4188900, remaining runtime: 174 s vol 0.86 imb F 1% step 4189000, remaining runtime: 174 s vol 0.86 imb F 5% step 4189100, remaining runtime: 174 s vol 0.87 imb F 4% step 4189200, remaining runtime: 173 s vol 0.88 imb F 6% step 4189300, remaining runtime: 173 s vol 0.85 imb F 1% step 4189400, remaining Bo Du Department of Polymer Science and Engineering, School of Chemical Engineering and technology, Tianjin University, Weijin Road 92, Nankai District 300072, Tianjin City P. R. China Tel/Fax: +86-22-27404303 E-mail: 2008d...@gmail.com -- gmx-users mailing listgmx-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
Re: [gmx-users] Adjust the screen's output frequency
On 2011-10-02 17:14, 杜波 wrote: How to change the screen's output frequency? ol 0.85 imb F 6% step 4188000, remaining runtime: 174 s vol 0.87 imb F 3% step 4188100, remaining runtime: 174 s vol 0.86 imb F 1% step 4188200, remaining runtime: 174 s vol 0.86 imb F 4% step 4188300, remaining runtime: 174 s vol 0.88 imb F 6% step 4188400, remaining runtime: 174 s vol 0.87 imb F 3% step 4188500, remaining runtime: 174 s vol 0.88 imb F 8% step 4188600, remaining runtime: 174 s vol 0.88 imb F 6% step 4188700, remaining runtime: 174 s vol 0.86 imb F 3% step 4188800, remaining runtime: 174 s vol 0.87 imb F 4% step 4188900, remaining runtime: 174 s vol 0.86 imb F 1% step 4189000, remaining runtime: 174 s vol 0.86 imb F 5% step 4189100, remaining runtime: 174 s vol 0.87 imb F 4% step 4189200, remaining runtime: 173 s vol 0.88 imb F 6% step 4189300, remaining runtime: 173 s vol 0.85 imb F 1% step 4189400, remaining mdrun -h Bo Du Department of Polymer Science and Engineering, School of Chemical Engineering and technology, Tianjin University, Weijin Road 92, Nankai District 300072, Tianjin City P. R. China Tel/Fax: +86-22-27404303 E-mail: 2008d...@gmail.com -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-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
[gmx-users] g_clustsize and temp.xvg
According to the description of the g_clustsize utility, it should create the file "temp.xvg" containing the temperature of the largest cluster versus time. While other files from g_clustsize are created correctly, the "temp.xvg" is always empty. What is printed follows: --- # This file was created Sun Oct 2 21:08:45 2011 # by the following command: # g_clustsize -n index.ndx # # g_clustsize is part of G R O M A C S: # # Good ROcking Metal Altar for Chronical Sinners # @title "Temperature of largest cluster" @xaxis label "Time (ps)" @yaxis label "T (K)" @TYPE xy --- The invocation line is: g_clustsize -n index.ndx Did anybody see this function working? I am using 4.0.7 version. -- Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA -- gmx-users mailing listgmx-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
Re: [gmx-users] g_clustsize and temp.xvg
On 3/10/2011 1:55 PM, Dr. Vitaly V. Chaban wrote: According to the description of the g_clustsize utility, it should create the file "temp.xvg" containing the temperature of the largest cluster versus time. While other files from g_clustsize are created correctly, the "temp.xvg" is always empty. What is printed follows: --- # This file was created Sun Oct 2 21:08:45 2011 # by the following command: # g_clustsize -n index.ndx # # g_clustsize is part of G R O M A C S: # # Good ROcking Metal Altar for Chronical Sinners # @title "Temperature of largest cluster" @xaxis label "Time (ps)" @yaxis label "T (K)" @TYPE xy --- The invocation line is: g_clustsize -n index.ndx Did anybody see this function working? I am using 4.0.7 version. Does your trajectory have velocities? Mark -- gmx-users mailing listgmx-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
