[gmx-users] On the usage of SD integrator as the thermostat
By 'proper dynamics' I mean the correct dynamics. For example, if a simulation with the SD integrator indicates that loop1 folds before loop2 folds, then this might be incorrect. The state information will be correct in velocity Langevin dynamics but the dynamic information might be incorrect. The advantage of the SD integrator over the Berendsen thermostat is that you get the correct ensemble. Check out papers by Garcia in relation to the flying ice cube problem and lipid bilayers. Is the same thing true for Nose-Hoover? I am not sure, but I am sure that you can find out. I recall hearing that the Nose-Hoover thermostat is very sensitive to propagating and magnifying temperature fluctuations. Chris. -- original message -- I am wondering what you mean by 'proper dynamics', Chris? And in general, what's the advantage of using sd integrator over md integrator together with Nose-Hoover thermostat. Thanks, km. On Fri, Nov 23, 2012 at 5:43 PM, Christopher Neale wrote: > I use the SD integrator with tau_t = 1.0 ps for all of my work, including > proteins in aqueous solution > or embedded in a lipid membrane. > > Any value of tau-t is "correct", and none will give you the proper dynamics, > but I find that the diffusion of > both water and lipids is quite reasonable when using tau_t=1.0 ps. > > I arrived at 1.0 ps after some help from Berk Hess on this list. I suggest > that you search out those old posts. > > Chris. > > -- original message -- > > In manual I've found possibility of the usage of the sd (langeven's > dynamics) integrator as the thermostat. > > It's known that friction coefficient in the Langeven's equations is > defined as m/Tau_t. So the high values of tau t can be appropriate > for the modeling of the thermostat without t_coupl. Also I know that > friction coefficient for such simulation must corresponds to the > viscosity of the system. In Gromacs manual I've found that Tau-t= 2.0 > ps can be appropriate value for such simulations. Does this value > suitable for water-soluble system only ? What Tau_t should I use for > modeling of the membrane proteins in the lipid-water environment which > has higher viscosity ? > > > Thanks for help, > > James -- 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] On the usage of SD integrator as the thermostat
I am wondering what you mean by 'proper dynamics', Chris? And in general, what's the advantage of using sd integrator over md integrator together with Nose-Hoover thermostat. Thanks, km. On Fri, Nov 23, 2012 at 5:43 PM, Christopher Neale wrote: > I use the SD integrator with tau_t = 1.0 ps for all of my work, including > proteins in aqueous solution > or embedded in a lipid membrane. > > Any value of tau-t is "correct", and none will give you the proper dynamics, > but I find that the diffusion of > both water and lipids is quite reasonable when using tau_t=1.0 ps. > > I arrived at 1.0 ps after some help from Berk Hess on this list. I suggest > that you search out those old posts. > > Chris. > > -- original message -- > > In manual I've found possibility of the usage of the sd (langeven's > dynamics) integrator as the thermostat. > > It's known that friction coefficient in the Langeven's equations is > defined as m/Tau_t. So the high values of tau t can be appropriate > for the modeling of the thermostat without t_coupl. Also I know that > friction coefficient for such simulation must corresponds to the > viscosity of the system. In Gromacs manual I've found that Tau-t= 2.0 > ps can be appropriate value for such simulations. Does this value > suitable for water-soluble system only ? What Tau_t should I use for > modeling of the membrane proteins in the lipid-water environment which > has higher viscosity ? > > > Thanks for help, > > James > -- > 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
[gmx-users] On the usage of SD integrator as the thermostat
I use the SD integrator with tau_t = 1.0 ps for all of my work, including proteins in aqueous solution or embedded in a lipid membrane. Any value of tau-t is "correct", and none will give you the proper dynamics, but I find that the diffusion of both water and lipids is quite reasonable when using tau_t=1.0 ps. I arrived at 1.0 ps after some help from Berk Hess on this list. I suggest that you search out those old posts. Chris. -- original message -- In manual I've found possibility of the usage of the sd (langeven's dynamics) integrator as the thermostat. It's known that friction coefficient in the Langeven's equations is defined as m/Tau_t. So the high values of tau t can be appropriate for the modeling of the thermostat without t_coupl. Also I know that friction coefficient for such simulation must corresponds to the viscosity of the system. In Gromacs manual I've found that Tau-t= 2.0 ps can be appropriate value for such simulations. Does this value suitable for water-soluble system only ? What Tau_t should I use for modeling of the membrane proteins in the lipid-water environment which has higher viscosity ? Thanks for help, James -- 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
