Sorry. I thought it was related to Boltzmann constt. Then how is 'k' calculated ?
On Wed, Mar 13, 2013 at 8:17 PM, Mark Abraham <mark.j.abra...@gmail.com>wrote: > k is dimensionless. It does not relate to Boltzmann's constant. The > exponential spacing it produces would lead to replica exchange rates that > are constant over the T range, under certain assumptions (e.g. papers by > David A Kofke). In practice, it normally would not lead to such rates. > Whether constant exchange rate is even useful/meaningful is another matter > (e.g. papers by Walter Nadler & Ulrich Hansmann). > > Mark > > On Wed, Mar 13, 2013 at 12:49 PM, Nikunj Maheshwari < > nixcrazyfor...@gmail.com> wrote: > > > I think determining k in the equation is not clear. How is it related to > a > > system size? If k=1/(kb.t) [kb=boltzmann constt], then for a given > starting > > temperature, the temp. spacing will be the same. Is that correct? > > > > On Wed, Mar 13, 2013 at 5:02 PM, Mark Abraham <mark.j.abra...@gmail.com > > >wrote: > > > > > On Wed, Mar 13, 2013 at 11:24 AM, Nikunj Maheshwari < > > > nixcrazyfor...@gmail.com> wrote: > > > > > > > Dear all. > > > > > > > > We are trying to run REMD on two proteins : 292 and 44 aa residues > > using > > > > GROMACS 4.6. > > > > We are unable to obtain the temperature spacing using REMD > temperature > > > > generator (http://folding.bmc.uu.se/remd/) as it is giving myriad > > > > temperature ranges (in the order of 150 for 250-550K range) > > > > > > > > > > Sounds normal for the kind of system you seem to have. Higher numbers > of > > > degrees of freedom require closer temperature spacing. > > > > > > Is there any other way to determine the spacing? Can the equation > > > > T(i)=T(0).e(k.i) be used, as we are unable to comprehend it? > > > > > > > > > > Yes, but if you want exchanges to occur, there are constraints on the > > size > > > of k. What's so hard about T(i+1)=T(i)*k? > > > > > > Mark > > > -- > > > gmx-users mailing list gmx-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 > > > > > -- > > gmx-users mailing list gmx-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 > > > -- > gmx-users mailing list gmx-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 > -- gmx-users mailing list gmx-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
