Re: [gmx-users] Energy minimization steps
Thank you Alex and Mark for your replies. :-) Azeem > Hi, > > How many steps does it take you to walk down a mountain to a certain > village? :-) Depends where you are on the mountain, and what's in the way. > But if all you need is to be somewhere near the valley floor to start > equilibration, anything goes! > > Mark > > On Wed, 21 Dec 2016 17:11 Alexwrote: > >> This isn't a Gromacs-specific parameter, or, for that matter, anything >> that straightforwardly depends on the nature of the system >> (solid/fluid/protein/lipid, etc) and its size, aside from maybe trivial >> cases. The max number of minimization steps is something that limits an >> energy minimization attempt, given the minimization algorithm, >> tolerance, the energy step, and, of course, how well-behaved you expect >> your system to be. It is a reasonable trial and error guess aimed at >> computational efficiency, e.g. not exceeding a certain amount of >> computational burden for really bad structures. Alternatively, limiting >> the number of minimization steps can help not produce some kind of a >> freaky structure when you have several local minima nearby. >> >> >> Alex >> >> >> On 12/20/2016 10:51 PM, Syed Azeem wrote: >> > Hi all, >> > >> > What is the basis of inputting the maximum number of energy >> > minimization steps in GROMACS? >> > Does maximum number of energy minimization steps depend on the number >> > of residues? >> > >> > I came across many articles wherein the authors have described the >> > number of energy minimization steps within which they have minimized >> > their protein. >> > >> > I have a protein of 596 residues to be simulated. >> > >> > Thanks in advance >> > >> > Azeem >> -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Energy minimization steps
Hi, How many steps does it take you to walk down a mountain to a certain village? :-) Depends where you are on the mountain, and what's in the way. But if all you need is to be somewhere near the valley floor to start equilibration, anything goes! Mark On Wed, 21 Dec 2016 17:11 Alexwrote: > This isn't a Gromacs-specific parameter, or, for that matter, anything > that straightforwardly depends on the nature of the system > (solid/fluid/protein/lipid, etc) and its size, aside from maybe trivial > cases. The max number of minimization steps is something that limits an > energy minimization attempt, given the minimization algorithm, > tolerance, the energy step, and, of course, how well-behaved you expect > your system to be. It is a reasonable trial and error guess aimed at > computational efficiency, e.g. not exceeding a certain amount of > computational burden for really bad structures. Alternatively, limiting > the number of minimization steps can help not produce some kind of a > freaky structure when you have several local minima nearby. > > > Alex > > > On 12/20/2016 10:51 PM, Syed Azeem wrote: > > Hi all, > > > > What is the basis of inputting the maximum number of energy > > minimization steps in GROMACS? > > Does maximum number of energy minimization steps depend on the number > > of residues? > > > > I came across many articles wherein the authors have described the > > number of energy minimization steps within which they have minimized > > their protein. > > > > I have a protein of 596 residues to be simulated. > > > > Thanks in advance > > > > Azeem > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Energy minimization steps
This isn't a Gromacs-specific parameter, or, for that matter, anything that straightforwardly depends on the nature of the system (solid/fluid/protein/lipid, etc) and its size, aside from maybe trivial cases. The max number of minimization steps is something that limits an energy minimization attempt, given the minimization algorithm, tolerance, the energy step, and, of course, how well-behaved you expect your system to be. It is a reasonable trial and error guess aimed at computational efficiency, e.g. not exceeding a certain amount of computational burden for really bad structures. Alternatively, limiting the number of minimization steps can help not produce some kind of a freaky structure when you have several local minima nearby. Alex On 12/20/2016 10:51 PM, Syed Azeem wrote: Hi all, What is the basis of inputting the maximum number of energy minimization steps in GROMACS? Does maximum number of energy minimization steps depend on the number of residues? I came across many articles wherein the authors have described the number of energy minimization steps within which they have minimized their protein. I have a protein of 596 residues to be simulated. Thanks in advance Azeem -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Energy minimization steps
Hi all, What is the basis of inputting the maximum number of energy minimization steps in GROMACS? Does maximum number of energy minimization steps depend on the number of residues? I came across many articles wherein the authors have described the number of energy minimization steps within which they have minimized their protein. I have a protein of 596 residues to be simulated. Thanks in advance Azeem -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.