Re: [gmx-users] Decreasing MSD of ligand ?
Chih-Ying Lin wrote: Hi The MSD decrease occurs in the long times. The ligand has bounded to a protein. How can the decrease happen? Probably because the ligand, being bound to the protein, has its motion restricted by its interaction with the protein. I don't see the purpose of measuring the MSD of a bound compound, since it probably shouldn't change much, anyway, if the ligand remains in the active site. MSD is much more useful for measuring the movement of more freely-diffusible entities (solvents, lipids, etc). -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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/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/mailing_lists/users.php
[gmx-users] Decreasing MSD of ligand ?
Hi The MSD decrease occurs in the long times. The ligand has bounded to a protein. How can the decrease happen? Thank you Lin Chih-Ying Lin wrote: > > > > HI MSD = mean square displacement diffusion coefficient = d/dt (MSD) I > simulate the protein and ligand system and then calculate the MSD of the > ligand. Then, i drew the plot of the time evolution of the MSD. But the > the MSD decreases as time for some period. I see nothing about my > codings. Would you please tell me about any possible errors i made? MSD can decrease due to insufficient sampling (time of the simulation, number of frames analyzed, etc). Depending on what you define as "some period" (during the initial part of the simulation? the middle? the end?) the behavior may or may not be normal, but from the few details you provide, there's no way to know. What do you hope to see in this analysis? Will a ligand bound to a protein really diffuse that much anyway? -Justin > Thank you Lin > > > > > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Decreasing MSD of ligand ?
Is the decrease occurs in the long times? Omer. On Tue, Nov 17, 2009 at 21:08, Chih-Ying Lin wrote: > > > > HI MSD = mean square displacement diffusion coefficient = d/dt (MSD) I > simulate the protein and ligand system and then calculate the MSD of the > ligand. Then, i drew the plot of the time evolution of the MSD. But the the > MSD decreases as time for some period. I see nothing about my codings. Would > you please tell me about any possible errors i made? Thank you Lin > > > > > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Decreasing MSD of ligand ?
Chih-Ying Lin wrote: HI MSD = mean square displacement diffusion coefficient = d/dt (MSD) I simulate the protein and ligand system and then calculate the MSD of the ligand. Then, i drew the plot of the time evolution of the MSD. But the the MSD decreases as time for some period. I see nothing about my codings. Would you please tell me about any possible errors i made? MSD can decrease due to insufficient sampling (time of the simulation, number of frames analyzed, etc). Depending on what you define as "some period" (during the initial part of the simulation? the middle? the end?) the behavior may or may not be normal, but from the few details you provide, there's no way to know. What do you hope to see in this analysis? Will a ligand bound to a protein really diffuse that much anyway? -Justin Thank you Lin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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/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/mailing_lists/users.php
[gmx-users] Decreasing MSD of ligand ?
HI MSD = mean square displacement diffusion coefficient = d/dt (MSD) I simulate the protein and ligand system and then calculate the MSD of the ligand. Then, i drew the plot of the time evolution of the MSD. But the the MSD decreases as time for some period. I see nothing about my codings. Would you please tell me about any possible errors i made? Thank you Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
