[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-tp499

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

[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 pro

[gmx-users] Re: Final state not reached in pulling simulation

Dear Stephan, Actually I had less idea about the force parameters of the pulling simulation, that's why I started with this force. I will again retry by reducing the force to 1000 and 100 KJmol/nm-2 too. Any suggestion regarding the other parameters is also welcome!! Thanks for your response!! -

[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 rega