Thanks a lot sir for your reply. Since experiments take place over hours but the simulations can at best approach millisecond levels. I was wondering if there is an acceptable time conversion factor from experiments to simulations. For example, the simulation data generated over a 350 ns period can be taken as an acceptable representation of a 24 hours long experiment.
On Wed, Feb 12, 2020 at 12:52 PM John Whittaker < johnwhitt...@zedat.fu-berlin.de> wrote: > > Dear group members > > > > My sincere apologies for the non-Gromacs related question, but I require > > this information urgently and hence posted my query here. > > > > Could someone please provide me with any guidelines to appropriately > model > > experimental processes with molecular dynamics simulations? > > What experimental processes are you talking about? Most timescales of > interest for physical processes range from picoseconds to seconds to > thousands of years. As you note, most timescales are out of reach of MD > (simulating anything interesting over the microsecond timescale is > extremely difficult). > > > > > Since the simulation periods are usually much shorter than the > > experimental > > time scales, I was searching for a generally acceptable time reduction > > factor or some literature towards that direction. > > What do you mean by "time reduction factor"? What exactly are you doing? > There are enhanced sampling methods which sort of "accelerate" the pace of > the process/system you are studying... Perhaps looking in that direction > might give you some ideas. > > Best, > > John > > > > > Any information or suggestion would be greatly appreciated. > > > > -- > > Cheers > > Peter > > -- > > 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. > -- Cheers Peter -- 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.