Right, I have a pdb where some of the residues are missing and when I try to simulate it I get LINCS warning in between the atom of the two ends of missing residues. So if I use a smaller time step (0.01) for final production run and energy minimization with setting constraint = none, making it computationally more expensive. Will these results will be O.K. Shahid Nayeem
On Fri, Aug 17, 2012 at 9:37 AM, Mark Abraham <mark.abra...@anu.edu.au> wrote: > On 17/08/2012 2:02 PM, shahid nayeem wrote: >> >> Dear all >>> >>> One basic clarification. How does LINCS algorithm influences the results >>> of final production run. In what respect a minimization, pr and final >>> simulation done with constraints = none and with constraint= all_bonds >>> are >>> different. > > > Sounds like you should do some background reading on how and why constraints > work. Manual and refs therein are good starting points. Or your favourite > molecular simulation textbook. In a nutshell, you use them in production > simulation because they're a reasonable model and allow a larger time step. > You might avoid them when you're not yet at equilbrium, because their > implementation can be brittle when your structure doesn't agree with the > model physics. > > Mark > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * 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 list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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
