Re: [gmx-users] Initial velocity
Thanks so much for your support, The point is that, I have this mathematical theory on coarse grain simulation for which is supposed to resolve the potential existing between atoms suspended by an angle theta(like the triangle share for two atoms). To solve for the potential, the theta between these two atoms has to be resolved first and then with the use of some functions in the math.h(acos,math.pow,log) I get the final potential. The mathematical model has been resolved and I have coded everything in C. When I made inquiries on how to implement it in GROMACS, I learnt that I have to modify the bondfree.c file in ./src/gmxlib directory. Theta is found based on the euclidian distance property and some differentiation afterwards and this theta is then supplied together with initial coordinates of the two atoms, boltzmann constant, and the mixing paramter (fine grain + coarse grain) and then the potential is supposed to be found. My supervisor seems not to be remembering what he did some years ago with GROMACS and it is really making life a though thing for me now I hope this information will be useful, let me know if I still need to clarify myself more pls. The whole idea is the determine the potential existing between fine-grain and coarse-grain multiscalled simulation Thanks so much On 13 May 2013 05:48, Acoot Brett acootbr...@yahoo.com wrote: Dear All, Will you please explain how the initial velocity may affect the MD results? What the initial velocity really means? How the velocity of the atoms in the protein changes in the MD process? What is the reasonable scope of the initial velocity? Any suggestions on how to manually input a defined initial velocity? Cheers, Acoot -- 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 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] Initial velocity
On 5/13/13 1:48 AM, Acoot Brett wrote: Dear All, Will you please explain how the initial velocity may affect the MD results? We use different initial velocities to improve sampling, i.e. to allow the trajectory to evolve in different ways. In the end, in the limit of infinite sampling, the trajectory ensemble averages should be the same. What the initial velocity really means? Just what it claims to be - the initial (first) velocities of each atom. How the velocity of the atoms in the protein changes in the MD process? Please read about MD integration algorithms. What is the reasonable scope of the initial velocity? I don't know what this means. Any suggestions on how to manually input a defined initial velocity? Provide grompp with an input file that has velocities - .trr, .edr, .gro, .cpt. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 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] Initial velocity
Please thanks so much for your support but I still do not get what all you are talking about is On 13 May 2013 11:44, Justin Lemkul jalem...@vt.edu wrote: On 5/13/13 1:48 AM, Acoot Brett wrote: Dear All, Will you please explain how the initial velocity may affect the MD results? We use different initial velocities to improve sampling, i.e. to allow the trajectory to evolve in different ways. In the end, in the limit of infinite sampling, the trajectory ensemble averages should be the same. What the initial velocity really means? Just what it claims to be - the initial (first) velocities of each atom. How the velocity of the atoms in the protein changes in the MD process? Please read about MD integration algorithms. What is the reasonable scope of the initial velocity? I don't know what this means. Any suggestions on how to manually input a defined initial velocity? Provide grompp with an input file that has velocities - .trr, .edr, .gro, .cpt. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] Initial velocity
On 5/13/13 9:45 AM, Brighter Agyemang wrote: Please thanks so much for your support but I still do not get what all you are talking about is These posts are not related to your question. Reading posts on other topics can be very informative and should be augmented by literature and textbook reading. -Justin On 13 May 2013 11:44, Justin Lemkul jalem...@vt.edu wrote: On 5/13/13 1:48 AM, Acoot Brett wrote: Dear All, Will you please explain how the initial velocity may affect the MD results? We use different initial velocities to improve sampling, i.e. to allow the trajectory to evolve in different ways. In the end, in the limit of infinite sampling, the trajectory ensemble averages should be the same. What the initial velocity really means? Just what it claims to be - the initial (first) velocities of each atom. How the velocity of the atoms in the protein changes in the MD process? Please read about MD integration algorithms. What is the reasonable scope of the initial velocity? I don't know what this means. Any suggestions on how to manually input a defined initial velocity? Provide grompp with an input file that has velocities - .trr, .edr, .gro, .cpt. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul, Ph.D. Research Scientist 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 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] Initial velocity
Dear All, Will you please explain how the initial velocity may affect the MD results? What the initial velocity really means? How the velocity of the atoms in the protein changes in the MD process? What is the reasonable scope of the initial velocity? Any suggestions on how to manually input a defined initial velocity? Cheers, Acoot -- 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
