Re: [gmx-users] Steered MD in reverse direction?
Thanks for the suggestion. Also, I was wondering how one can get the time profile of the irreversible work from the gromacs pull-code out put . From constant pulling-rate SMD, we get time profile of force pullf.xvg and pullx.xvg. I wonder does multiplying the the value from pullx.xvg and value from pullf.xvg will provide the work . Or, will it be force ( obtained from pullf.xvg) multiplied by pulling rate multiplied by time ? From: Justin A. Lemkul jalem...@vt.edu To: Sanku M msank...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, November 3, 2011 9:27 PM Subject: Re: [gmx-users] Steered MD in reverse direction? Sanku M wrote: Hi, I am performing steered Molecular dynamics simulation to pull a molecule out of a complex. I am using gromacs 4.5.4 to perform the constant rate pulling..I have done the steered MD simulation in a particular direction i.e hav pulled the molecule out of complex. But, to check the convergence/hysterisis of the pulled path way, I would like to perform the same steered MD in reverse direction i.e push the molecule back into the complex. But, I was wondering, to perform the backward steered MD, how should I modify the .mdp parameters? Should I make the pull_rate1 negative or switch the pull_group0 and pull_group1 ? Any help will be appreciated. Use a negative pull rate. But simple pulling like this can be difficult; you're now trying to hit a moving target. A slight rotation of the protein can render the whole simulation junk - your pulled molecule may smack into some undesired location. -Justin The following is the part of the pull-code parameter I am using: ; Pull code pull = umbrella pull_geometry = distance ; simple distance increase pull_dim = N N Y pull_start = yes ; define initial COM distance 0 pull_ngroups = 1 pull_group0 = Mol_A pull_group1 = Mol_B pull_rate1 = 0.0025 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 1000 ; kJ mol^-1 nm^-2 Sanku -- 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 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] Steered MD in reverse direction?
Sanku M wrote: Hi, I am performing steered Molecular dynamics simulation to pull a molecule out of a complex. I am using gromacs 4.5.4 to perform the constant rate pulling..I have done the steered MD simulation in a particular direction i.e hav pulled the molecule out of complex. But, to check the convergence/hysterisis of the pulled path way, I would like to perform the same steered MD in reverse direction i.e push the molecule back into the complex. But, I was wondering, to perform the backward steered MD, how should I modify the .mdp parameters? Should I make the pull_rate1 negative or switch the pull_group0 and pull_group1 ? Any help will be appreciated. Use a negative pull rate. But simple pulling like this can be difficult; you're now trying to hit a moving target. A slight rotation of the protein can render the whole simulation junk - your pulled molecule may smack into some undesired location. -Justin The following is the part of the pull-code parameter I am using: ; Pull code pull= umbrella pull_geometry = distance ; simple distance increase pull_dim= N N Y pull_start = yes ; define initial COM distance 0 pull_ngroups= 1 pull_group0 = Mol_A pull_group1 = Mol_B pull_rate1 = 0.0025 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 1000 ; kJ mol^-1 nm^-2 Sanku -- 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 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] Steered MD in reverse direction?
Thanks for the suggestion. Also, I was wondering how one can get the time profile of the irreversible work from the gromacs pull-code out put . From constant pulling-rate SMD, we get time profile of force pullf.xvg and pullx.xvg. I wonder does multiplying the the value from pullx.xvg and value from pullf.xvg will provide the work . Or, will it be force ( obtained from pullf.xvg) multiplied by pulling rate multiplied by time ? From: Justin A. Lemkul jalem...@vt.edu To: Sanku M msank...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, November 3, 2011 9:27 PM Subject: Re: [gmx-users] Steered MD in reverse direction? Sanku M wrote: Hi, I am performing steered Molecular dynamics simulation to pull a molecule out of a complex. I am using gromacs 4.5.4 to perform the constant rate pulling..I have done the steered MD simulation in a particular direction i.e hav pulled the molecule out of complex. But, to check the convergence/hysterisis of the pulled path way, I would like to perform the same steered MD in reverse direction i.e push the molecule back into the complex. But, I was wondering, to perform the backward steered MD, how should I modify the .mdp parameters? Should I make the pull_rate1 negative or switch the pull_group0 and pull_group1 ? Any help will be appreciated. Use a negative pull rate. But simple pulling like this can be difficult; you're now trying to hit a moving target. A slight rotation of the protein can render the whole simulation junk - your pulled molecule may smack into some undesired location. -Justin The following is the part of the pull-code parameter I am using: ; Pull code pull = umbrella pull_geometry = distance ; simple distance increase pull_dim = N N Y pull_start = yes ; define initial COM distance 0 pull_ngroups = 1 pull_group0 = Mol_A pull_group1 = Mol_B pull_rate1 = 0.0025 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 1000 ; kJ mol^-1 nm^-2 Sanku -- 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 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
