Re: [gmx-users] question on KALP-15 in DPPC tutorial
Thank you Mark and Justin. Yes i did check the reference of your tutorial, but its just that there are so many groups using same FF but different cut-off lengths. amit On Sun, Nov 21, 2010 at 10:22 AM, Justin A. Lemkul wrote: > Quoting Mark Abraham : > > > On 21/11/2010 8:45 PM, Amit Choubey wrote: > > > Hi all, > > > > > > I was going through the very nicely presented tutorial by Justin (on > > > KALP-15 in DPPC). I have one question regarding the non-bonded > > > cut-offs. It seems that people use many different values of non-bonded > > > cut-off (varying from 0.9 nm to 1.2 nm or probably more). How should i > > > choose the cut-off values for my simulations ? > > > > In the first instance, by reproducing the conditions under which the > > parameters were validated. Unfortunately, most of the force fields were > > not parametrized for PME, under which they are often now used. So look > > at some papers from large well-known groups that have done something > > similar to what you want to do, judge how well they have worked, and do > > something comparable. Unfortunately, there have been little or no > > systematic studies of how accurate forcefield X plus PME needs to be to > > model reality usefully. Hopefully that will change :-) > > > > And directly related to the tutorial in question, the settings used therein > were > assigned to reproduce the study that I cite in the introductory material. > > -Justin > > > > 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 > -- 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] question on KALP-15 in DPPC tutorial
Quoting Mark Abraham : > On 21/11/2010 8:45 PM, Amit Choubey wrote: > > Hi all, > > > > I was going through the very nicely presented tutorial by Justin (on > > KALP-15 in DPPC). I have one question regarding the non-bonded > > cut-offs. It seems that people use many different values of non-bonded > > cut-off (varying from 0.9 nm to 1.2 nm or probably more). How should i > > choose the cut-off values for my simulations ? > > In the first instance, by reproducing the conditions under which the > parameters were validated. Unfortunately, most of the force fields were > not parametrized for PME, under which they are often now used. So look > at some papers from large well-known groups that have done something > similar to what you want to do, judge how well they have worked, and do > something comparable. Unfortunately, there have been little or no > systematic studies of how accurate forcefield X plus PME needs to be to > model reality usefully. Hopefully that will change :-) > And directly related to the tutorial in question, the settings used therein were assigned to reproduce the study that I cite in the introductory material. -Justin 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] question on KALP-15 in DPPC tutorial
On 21/11/2010 8:45 PM, Amit Choubey wrote: Hi all, I was going through the very nicely presented tutorial by Justin (on KALP-15 in DPPC). I have one question regarding the non-bonded cut-offs. It seems that people use many different values of non-bonded cut-off (varying from 0.9 nm to 1.2 nm or probably more). How should i choose the cut-off values for my simulations ? In the first instance, by reproducing the conditions under which the parameters were validated. Unfortunately, most of the force fields were not parametrized for PME, under which they are often now used. So look at some papers from large well-known groups that have done something similar to what you want to do, judge how well they have worked, and do something comparable. Unfortunately, there have been little or no systematic studies of how accurate forcefield X plus PME needs to be to model reality usefully. Hopefully that will change :-) Mark -- 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] question on KALP-15 in DPPC tutorial
Hi all, I was going through the very nicely presented tutorial by Justin (on KALP-15 in DPPC). I have one question regarding the non-bonded cut-offs. It seems that people use many different values of non-bonded cut-off (varying from 0.9 nm to 1.2 nm or probably more). How should i choose the cut-off values for my simulations ? amit -- 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
