Re: [gmx-users] How to calculate the center of the mass in gromacs
Thanks a lot, Justin. It works well. Jerry --- On Tue, 5/15/12, Justin A. Lemkul wrote: From: Justin A. Lemkul Subject: Re: [gmx-users] How to calculate the center of the mass in gromacs To: "Discussion list for GROMACS users" Date: Tuesday, May 15, 2012, 12:51 PM On 5/15/12 11:35 AM, xu zhijun wrote: > Is there the simple method to calculate the center of the mass for a group of > atoms? > I want to post-process the traj date file. > This is a function of g_traj. -Justin -- Justin A. Lemkul, Ph.D. Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 -- 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] How to calculate the center of the mass in gromacs
Is there the simple method to calculate the center of the mass for a group of atoms? I want to post-process the traj date file. Thanks a lot. -- 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] Pull code for Constraint
Hi, I try to pull the small molecule from the bulk solution to the surface by the Constraint function. However, it seems that it does not work well. Here my part of run parameters about the Constraint in my mdp file ## constraints = all-bonds; hbonds; all-bonds constraint-algorithm = Lincs pull = constraint pull_geometry = distance pull_dim = N N Y pull_ngroups = 1 pull_group0 = Surface pull_group1 = Protein pull_nstxout = 1000 pull_nstfout = 1000 pull_rate1 = -0.001 pull_init1 = 1.73331 ## Based my understanding, the pull_rate1 is about -0.001/ps. That means in the pullx.xvg file, the distance shoud be as follows (only the z-distance shown, time step is 1fs.) 1.73331 1.72231 1.72131 1.72031 . . However, in my simulation, the results from the simulation is as follow: 1.73331 1.71154 1.75043 1.73213 1.78065 1.79769 1.84298 1.87008 It seems some force has been imposed on the pull molecules. But in the pullf.xvg the force is ZERO. I used the latest gromacs version, But for the gromacs4.0 it works very well (works as what I think). Can someone help me about the issue? Thanks a lot Jerry -- 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] How to the define the A and B states for the calculation of free energy
Thanks a lot Justin. Have a good night. PS: the gromacs tutorials in your home page are really pretty good. --- On Sat, 1/14/12, Justin A. Lemkul wrote: From: Justin A. Lemkul Subject: Re: [gmx-users] How to the define the A and B states for the calculation of free energy To: "Discussion list for GROMACS users" Date: Saturday, January 14, 2012, 8:04 PM xu zhijun wrote: > Thanks Justin. > > You mean I put the na+ and Ca+ in the same "moleculetype"？ > But I just worry about whether it is feasible to put the two ions in the same > moleculetypes even if they have no any connects between them (bond, angle). > The chemical definition of a molecule and the Gromacs definition of a moleculetype are completely unrelated. In theory, you could put all of the molecules in your system in a single moleculetype. It's simply a topology construct for organization. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 -- 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] How to the define the A and B states for the calculation of free energy
Thanks Justin. You mean I put the na+ and Ca+ in the same "moleculetype"？ But I just worry about whether it is feasible to put the two ions in the same moleculetypes even if they have no any connects between them (bond, angle). Thanks again. --- On Sat, 1/14/12, Justin A. Lemkul wrote: From: Justin A. Lemkul Subject: Re: [gmx-users] How to the define the A and B states for the calculation of free energy To: "Discussion list for GROMACS users" Date: Saturday, January 14, 2012, 7:33 PM xu zhijun wrote: > Hi gromacs-users, > > I have carefully checked the manual about the define the A and B states for > the calcualtion of free energy. And I also known that "couple-moltype“ and > "couple-lambda0" and "couple-lambda1". > However I have two types of molecules for decoupling in the simulaiton. It > seems that Gromacs can not deal with more than one tpes of moleucle with the > "couple-moltype". > For example I want to decouple the Na+ and Ca+. Is the the other way to > define the decoupling molecules? It seems that I can directly define the B > state in the top files for these two ions, repectively. If it is reasonable, > does the other molecules without the descrption of the B state keep fixed? (I > mean these molecuse will not involve the decoupling process in the > simulation.) > If there is not a defined B-state, then parameters from the A-state are applied, hence no transformation. Another approach is to hack the topology such that the ions you want to decouple are all in the same [moleculetype]. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 -- 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] How to the define the A and B states for the calculation of free energy
Hi gromacs-users, I have carefully checked the manual about the define the A and B states for the calcualtion of free energy. And I also known that "couple-moltype“ and "couple-lambda0" and "couple-lambda1". However I have two types of molecules for decoupling in the simulaiton. It seems that Gromacs can not deal with more than one tpes of moleucle with the "couple-moltype". For example I want to decouple the Na+ and Ca+. Is the the other way to define the decoupling molecules? It seems that I can directly define the B state in the top files for these two ions, repectively. If it is reasonable, does the other molecules without the descrption of the B state keep fixed? (I mean these molecuse will not involve the decoupling process in the simulation.) Thanks very much for any suggestions -- 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
