[gmx-users] Re: question on pulling 2 groups in afm run
Hi Linchen, You may want to try adding the line ngroups=2 to the pull.ppa, right under runtype = afm. It's in the new manual (version 3.3, section 6.2.3). Otherwise, I believe the number of groups defaults to 1, and that's why mdrun gets confused about finding a group_2, afm_rate2, etc. - it's only looking for one of each. I don't promise that will fix your problem, since I don't do much with pulling on multiple groups, but it's a good bet on a place to start. If that doesn't fix it, post the actual error messages. -Emily Walton Dear gromacs users, I met a problem on pulling 2 groups in a afm pulling run. When mdrun processes input file, error messages such as unknown left- hand : group_2 appear for group_2, afm_rate2, afm_k2, afm_dir2 and afm_init2. However, pulling one group is OK. My pull.ppa is verbose = yes runtype = afm group_1 = a_TER1 group_2 = a_TER2 pulldim = N N Y afm_rate1 = 0.01 afm_rate2 = 0.01 afm_k1= 1000 afm_k2= 1000 afm_dir1 = 0 0 1 afm_dir2 = 0 0 1 afm_init1 = 13.639 3.264 4.486 afm_init2 = 14.221 3.873 2.790 The group definition in pull.ndx is [ a_TER1 ] 1136 [ a_TER2 ] 2425 Could anyone tell me what's wrong here? Thanks a lot Best regards Linchen Gong -- ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users End of gmx-users Digest, Vol 25, Issue 40 * ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] afm pulling
Hi, Dear all, I am simulating an unbinding process with the pull code (afm option). I've been reading previous posts about this option and I just wanted to clarify some ideas and ask some questions. There are: 1-The pulling can be done choosing two different molecules. Why a particular group within a molecule can not be used? Not even as a reference group? Any group that is defined in your index file (specified with mdrun - pn pull.ndx) can be used. Look at made_ndx in the manual to learn how to add new groups. 2-Should I need to fixed the center of mass of the protein to avoid shifts? How can I do that? Would it be OK to use posre for the backbone of the protein with carrying out the pulling? It depends on what you want to do. Typically, something would need to be fixed. In ligand-protein systems, the center of mass of the protein is a reasonable choice. It was used by Grubmuller et al. in their 1996 Science paper on the unbinding of biotin-streptavidin. (Science, 271:954–5, 1996) For unraveling of proteins, one terminal atom may be fixed while the other is pulled. Fixing the center of mass of a group in the index file can be done in the .mdp file you feed to grompp. See the manual, chapter 7. 3-Should I removed all the constraints for the bonds (SHAKE, lincs)? I think this is a matter of preference. Some people do, some people don't. Again, it will depend on your system- is it stable without the constraints? The bonds that are broken with afm pulling are bonds described by non- bonded interaction terms in gromacs. These bonds wouldn't be constrained by shake or lincs anyway, so the presence or absence of constrains should have a minimal effect on the simulation results. 4-once I have the pull.pdo the calculation of the applied force will be F= K*(zspring -zgroup) (assuming I am pulling in the z direction)? Yes. The spring is an ideal spring, so force is k*(extension). The extension can be calculated from the pull.pdo file. -Emily Walton___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] pull.pdo AFM force
Hi all I have a short question. Could you please tell me what do the columns in pull.pdo (output file from AFM) stand for. Is there a simple way to obtain forces from AFM pulling? Thank you for help. Michal As an example, with one pulling group, and pulling in 3D, the output columns read: Time, Reference group X, Reference group Y, Reference group Z, Pull Group X, Pull Group Y, Pull Group Z, Spring X, Spring Y, Spring Z for a total of 10 columns. If you didn't pull in 3D, you'll only get output for the dimensions where pulldim was set to Y in your .ppa file. I'm not sure how multiple pull groups are handled. I have a script to calculate the forces for pull runs using only one pull group in 3 dimensions that I can share on request. -Emily Walton ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
