Re: [gmx-users] What is the subroutine for SHAKE or RATTLE? Thanks.
On 17/05/2012 11:48 AM, kevin wrote: Thanks. I think I should have a look at some specific documents to understand the flow of control. Namely, to understand what is purpose of the subroutines in src/mdlib/. But I could not find such information in the Gromacs user manual. Do anyone know such an document? Thanks. Unfortunately the development of GROMACS is not fast enough to suit anybody's wishes, and too fast and complex to make it worth people's volunteer time to do much beyond what can be observed by inspecting the code. I suggest you step through a run of GROMACS with your favourite debugger on a similar calculation and observe the control flow. There is some discussion of data structures on the GROMACS webpage which is more-or-less useful for the 4.0/4.5 series. Mark kevin.len *From:* Mark Abraham mailto:mark.abra...@anu.edu.au *Date:* 2012-05-16 13:57 *To:* Discussion list for GROMACS users mailto:gmx-users@gromacs.org *Subject:* Re: [gmx-users] What is the subroutine for SHAKE or RATTLE? Thanks. On 16/05/2012 12:28 PM, kevin wrote: Hi, everyone. It is my first use of Gromacs http://lammps.sandia.gov/ and I am looking for a numerical scheme for one specific constrained SDE, the constrain is a macroscopic one, i.e., overdamped Langevin(Brownian dynamics) equations with an equality constraint which is expressed in form of expectation(or moment of n-th order). This is unlike the common 'micro' constraint(simply function in terms of variable in SDE) . I can not find such a subrountine for solving constrained SDE in MD codes in Gromacs http://lammps.sandia.gov/. I see there is an algorithm called SHAKE or RATTLE which and it seems they could implement Langevin(or Brownian) dynamics with constraints. If convenient, could anyone help to point out which subroutine is specific for implementing SHAKE/RATTLE? Thanks in advance. Various files in src/mdlib/ deal with these kinds of algorithms. 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
Re: Re: [gmx-users] What is the subroutine for SHAKE or RATTLE? Thanks.
Thanks. I think I should have a look at some specific documents to understand the flow of control. Namely, to understand what is purpose of the subroutines in src/mdlib/. But I could not find such information in the Gromacs user manual. Do anyone know such an document? Thanks. kevin.len From: Mark Abraham Date: 2012-05-16 13:57 To: Discussion list for GROMACS users Subject: Re: [gmx-users] What is the subroutine for SHAKE or RATTLE? Thanks. On 16/05/2012 12:28 PM, kevin wrote: Hi, everyone. It is my first use of Gromacs and I am looking for a numerical scheme for one specific constrained SDE, the constrain is a macroscopic one, i.e., overdamped Langevin(Brownian dynamics) equations with an equality constraint which is expressed in form of expectation(or moment of n-th order). This is unlike the common 'micro' constraint(simply function in terms of variable in SDE) . I can not find such a subrountine for solving constrained SDE in MD codes in Gromacs. I see there is an algorithm called SHAKE or RATTLE which and it seems they could implement Langevin(or Brownian) dynamics with constraints. If convenient, could anyone help to point out which subroutine is specific for implementing SHAKE/RATTLE? Thanks in advance. Various files in src/mdlib/ deal with these kinds of algorithms. 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
Re: [gmx-users] What is the subroutine for SHAKE or RATTLE? Thanks.
On 16/05/2012 12:28 PM, kevin wrote: Hi, everyone. It is my first use of Gromacs http://lammps.sandia.gov/ and I am looking for a numerical scheme for one specific constrained SDE, the constrain is a macroscopic one, i.e., overdamped Langevin(Brownian dynamics) equations with an equality constraint which is expressed in form of expectation(or moment of n-th order). This is unlike the common 'micro' constraint(simply function in terms of variable in SDE) . I can not find such a subrountine for solving constrained SDE in MD codes in Gromacs http://lammps.sandia.gov/. I see there is an algorithm called SHAKE or RATTLE which and it seems they could implement Langevin(or Brownian) dynamics with constraints. If convenient, could anyone help to point out which subroutine is specific for implementing SHAKE/RATTLE? Thanks in advance. Various files in src/mdlib/ deal with these kinds of algorithms. 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
