[gmx-users] increasing simulation time via temperature rising
Hi all I'm studying effect of temperature on incredibly stable protein. I've started simulating at 300K then, 400K and 500K. 30ns simulating takes about 4days for these three temperature in a same system. when I want to run 30ns simulation at 600K, it will take more than 20 days does rising temperature, have any affect on time of simulation? is this increasing in time reasonable? thanks -- 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] increasing simulation time via temperature rising
Hi Nazli, No, that's not related to temperature. Otherwise you'd probably see a trend. I guess with the 600K simulation you have another process that interferes and eats CPU. Mind that a simulation running on four/eight cores will be affected significantly by anything that uses a considerable part of a CPU. Cheers, Tsjerk On May 18, 2015 08:48, nazli kashani javid nazlikja...@gmail.com wrote: Hi all I'm studying effect of temperature on incredibly stable protein. I've started simulating at 300K then, 400K and 500K. 30ns simulating takes about 4days for these three temperature in a same system. when I want to run 30ns simulation at 600K, it will take more than 20 days does rising temperature, have any affect on time of simulation? is this increasing in time reasonable? thanks -- 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] increasing simulation time via temperature rising
Hi Nazli, Also, I doubt simulations beyond 400 K make any sense: not only such conditions are implausible for a protein to exist in, but, as far as I know, the force fields are not parametrized to work so far beyond room temperature. cheers, M. 2015-05-18 9:05 GMT+02:00 Tsjerk Wassenaar tsje...@gmail.com: Hi Nazli, No, that's not related to temperature. Otherwise you'd probably see a trend. I guess with the 600K simulation you have another process that interferes and eats CPU. Mind that a simulation running on four/eight cores will be affected significantly by anything that uses a considerable part of a CPU. Cheers, Tsjerk On May 18, 2015 08:48, nazli kashani javid nazlikja...@gmail.com wrote: Hi all I'm studying effect of temperature on incredibly stable protein. I've started simulating at 300K then, 400K and 500K. 30ns simulating takes about 4days for these three temperature in a same system. when I want to run 30ns simulation at 600K, it will take more than 20 days does rising temperature, have any affect on time of simulation? is this increasing in time reasonable? thanks -- 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. -- 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.
