[gmx-users] Re: Final state not reached in pulling simulation
Dear Thomas, Thanks for ur reply. I have visualized my trajectory and found no water molecule in between. Moreover, there are no residues in between the Residue and GTP molecule too. I feel I have already applied a large force for the pulling. Still I will consider you suggestion. One query regarding your suggestion. It one happens to find a water molecule in between the pulling groups, will removal of that water be a solution, because during the course of simulation it may happen that some other molecule again come between? Thanks anyways for you reply and suggestions. --Neeru -- View this message in context: http://gromacs.5086.n6.nabble.com/Final-state-not-reached-in-pulling-simulation-tp4999387p4999396.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Re: Final state not reached in pulling simulation
Dear Justin, Thanks for the suggestion regarding the pull force. 1)I will try by reducing the pull force to 1000 and 100 KJmol/nm2 now. Regarding the force being applied in z-direction, after visualizing my trajectory i thought it would work by providing force in z-direction. 2)Regarding the protein rotation, it does not rotate over the time. There are just some localized changes in it. 3)Regarding the distance measurement, I am measuring the distance between the specific atoms of the residue and the atoms of the GTP. Till now, these distances as well as the overall protein geometry is maintained well in the range too. 4)If this kind of pulling does not work out in my case, I will again try it with using position geometry too with pull_vec1. Can you suggest why have I not reached the final distance at the end of the simulation? Is it because of the geometry that I have used, because the force constant is already too high in this case? Thanks again for your response. -- View this message in context: http://gromacs.5086.n6.nabble.com/Final-state-not-reached-in-pulling-simulation-tp4999387p4999399.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Re: Final state not reached in pulling simulation
On 7/13/12 2:32 AM, Neeru Sharma wrote: Dear Justin, Thanks for the suggestion regarding the pull force. 1)I will try by reducing the pull force to 1000 and 100 KJmol/nm2 now. Regarding the force being applied in z-direction, after visualizing my trajectory i thought it would work by providing force in z-direction. 2)Regarding the protein rotation, it does not rotate over the time. There are just some localized changes in it. 3)Regarding the distance measurement, I am measuring the distance between the specific atoms of the residue and the atoms of the GTP. Till now, these distances as well as the overall protein geometry is maintained well in the range too. 4)If this kind of pulling does not work out in my case, I will again try it with using position geometry too with pull_vec1. Can you suggest why have I not reached the final distance at the end of the simulation? Is it because of the geometry that I have used, because the force constant is already too high in this case? I don't know why this is happening. That's why you need to try more things to see if you can root out the issue. There are a whole host of factors that can act against the pulling force. You're not using any sort of position restraints, are you? The other thing to keep in mind is that if your initial distance is 0.7 nm, and you pull for 10 ns at 0.05 nm/ns, you should in theory end up with a distance of 0.2 nm, not 0.3 nm. That is, assuming that the pulled group is free to move and thus smoothly goes along with the spring. Other forces within the structure may act in opposition. -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 * Only plain text messages are allowed! * 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] Re: Final state not reached in pulling simulation
Thanks Justin for all your comments and suggestion. I am not using any position restraints as of now. But I will try out more parameters and more options. Thanks again. --Neeru -- View this message in context: http://gromacs.5086.n6.nabble.com/Final-state-not-reached-in-pulling-simulation-tp4999387p4999414.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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
