### RE: [gmx-users] stochastic dynamics , langevin

From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: RE: [gmx-users] stochastic dynamics , langevin Date: Thu, 23 Oct 2008 15:32:02 -0700 Along these same lines... (a)is there an thermostat setting in GROMACS that comes close to the DPD thermostat as described in (T. Soddemann, B. D¨unweg, and K. Kremer. Dissipative particle dynamics: A useful thermostat for equilibrium and nonequilibrium molecular dynamics simulations. Phys. Rev. E, 68:046702, 2003.) No. (b) if nothing approaches DPD, how would a one go about starting to write a new thermostat in GROMACS? Implementing a new thermostat in Gromacs is easy, except for DPD, since it interferes both with the neighborlist and the integration. I have considered implementing DPD, but it is a lot of work and also difficult to do efficiently, since the DPD interactions are more expensive that the Coulomb and LJ interactions. Note that you only really need DPD for non-equilibrium phenomena where hydrodynamics plays a role. Berk -Matt - Matthew Hoopes Biophysics Graduate Group University of California, Davis [EMAIL PROTECTED] 530-752-6452 - Hi, Brownina dynamics is a Langevin equation for the coordinates (no inertia). Stochastic dynamics is a Langevin equation for the velocities (with inertia). Everything depends on what you want to do, which you do not tell in detail. If you want to leave out the solvent, but you want to simulate a system in solvent, SD is not going to help you, since there is no implicit solvent potential, so your potential and therefore your sampling is nonsense. tau_t has no effect on the distribution, only on the dynamics. If you want the correct dynamics, you will have fit tau_t to reproduce some kinetic quantity that you are interested in. For different quantities tau_t can be different. Berk Date: Thu, 23 Oct 2008 15:31:16 +0200 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: [gmx-users] stochastic dynamics , langevin Dear All, I am trying to perform Langevin dynamics of large peptides / proteins. After reading the manual going over some old mails in this list, I have two points I hope you could clear for me: [Gromacs version 3.3.3] 1) I am a bit confused with Brownian vs. Langevin dynamics. Is this the proper keywords I should use for Langevin dynamics: integrator = sd ; bd-fric= 0 ; tau_t = 10 ; ref_t = 300 ; With bd-fric=0, the friction is taken as the inverse tau_t. 2) From your experience, what are good values of tau_t (or 1/tau_t) for simulating a protein? In 2006 list, David has commented that choosing tau_t is very important ( http://www.gromacs.org/pipermail/gmx-users/2006-July/023089.html ). Your help is appreciated. Omer. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php

### RE: [gmx-users] stochastic dynamics , langevin

Hi, Brownina dynamics is a Langevin equation for the coordinates (no inertia). Stochastic dynamics is a Langevin equation for the velocities (with inertia). Everything depends on what you want to do, which you do not tell in detail. If you want to leave out the solvent, but you want to simulate a system in solvent, SD is not going to help you, since there is no implicit solvent potential, so your potential and therefore your sampling is nonsense. tau_t has no effect on the distribution, only on the dynamics. If you want the correct dynamics, you will have fit tau_t to reproduce some kinetic quantity that you are interested in. For different quantities tau_t can be different. Berk Date: Thu, 23 Oct 2008 15:31:16 +0200 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: [gmx-users] stochastic dynamics , langevin Dear All, I am trying to perform Langevin dynamics of large peptides / proteins. After reading the manual going over some old mails in this list, I have two points I hope you could clear for me: [Gromacs version 3.3.3] 1) I am a bit confused with Brownian vs. Langevin dynamics. Is this the proper keywords I should use for Langevin dynamics: integrator = sd ; bd-fric= 0 ; tau_t = 10 ; ref_t = 300 ; With bd-fric=0, the friction is taken as the inverse tau_t. 2) From your experience, what are good values of tau_t (or 1/tau_t) for simulating a protein? In 2006 list, David has commented that choosing tau_t is very important ( http://www.gromacs.org/pipermail/gmx-users/2006-July/023089.html ). Your help is appreciated. Omer. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php

### Re: [gmx-users] stochastic dynamics , langevin

Thanks for the quick reply Berk. 1) Is this the proper keywords I should use for Langevin dynamics: integrator = sd ; bd-fric= 0 ; tau_t = 10 ; ref_t = 300 ; Basically, I want to know if I am using the 4 parameters correctly. That is - for Langevin dynamics, I should pick bd-fric=0, to allow the friction to be taken from 1/tau_t ? Secondly, I am looking for examples of tau_t different people use for different system. Thanks, Omer. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php

### Re: [gmx-users] stochastic dynamics , langevin

Berk Hess wrote: Everything depends on what you want to do, which you do not tell in detail. If you want to leave out the solvent, but you want to simulate a system in solvent, SD is not going to help you, since there is no implicit solvent potential, so your potential and therefore your sampling is nonsense. So can we assume that the sampling is equivalent to that in vacuum (as far as underlying potential/free energy surface is concerned), with only the dynamics being slowed down by the viscous drag? Also, is it a safe guideline to use Langevin dynamics for small particles in not so viscous fluid and Brownian dynamics for large particles in highly viscous fluid? Regards, Suman. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php

### RE: [gmx-users] stochastic dynamics , langevin

Along these same lines... (a)is there an thermostat setting in GROMACS that comes close to the DPD thermostat as described in (T. Soddemann, B. D¨unweg, and K. Kremer. Dissipative particle dynamics: A useful thermostat for equilibrium and nonequilibrium molecular dynamics simulations. Phys. Rev. E, 68:046702, 2003.) (b) if nothing approaches DPD, how would a one go about starting to write a new thermostat in GROMACS? -Matt - Matthew Hoopes Biophysics Graduate Group University of California, Davis [EMAIL PROTECTED] 530-752-6452 - Hi, Brownina dynamics is a Langevin equation for the coordinates (no inertia). Stochastic dynamics is a Langevin equation for the velocities (with inertia). Everything depends on what you want to do, which you do not tell in detail. If you want to leave out the solvent, but you want to simulate a system in solvent, SD is not going to help you, since there is no implicit solvent potential, so your potential and therefore your sampling is nonsense. tau_t has no effect on the distribution, only on the dynamics. If you want the correct dynamics, you will have fit tau_t to reproduce some kinetic quantity that you are interested in. For different quantities tau_t can be different. Berk Date: Thu, 23 Oct 2008 15:31:16 +0200 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: [gmx-users] stochastic dynamics , langevin Dear All, I am trying to perform Langevin dynamics of large peptides / proteins. After reading the manual going over some old mails in this list, I have two points I hope you could clear for me: [Gromacs version 3.3.3] 1) I am a bit confused with Brownian vs. Langevin dynamics. Is this the proper keywords I should use for Langevin dynamics: integrator = sd ; bd-fric= 0 ; tau_t = 10 ; ref_t = 300 ; With bd-fric=0, the friction is taken as the inverse tau_t. 2) From your experience, what are good values of tau_t (or 1/tau_t) for simulating a protein? In 2006 list, David has commented that choosing tau_t is very important ( http://www.gromacs.org/pipermail/gmx-users/2006-July/023089.html ). Your help is appreciated. Omer. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php