the protein has about 170 amino acid. On Wed, Nov 5, 2014 at 1:13 PM, Johnny Lu <[email protected]> wrote:
> The statistics was calculated for 80 ns of NVT simulation, after a 80 ns > NPT simulation. > > In papers, I saw people talked about using the average volume of a > previous NPT simulation to choose the frame with the correct volume. And > then, run NVT starting from the NPT frame. > But they don't talk about the pressure that they get in the NVT simulation > (even in a force field paper). > > I just want to know if the reviewer will be ok with my paper, if I mention > the pressure that I get in the NVT simulation. > > > On Wed, Nov 5, 2014 at 12:16 PM, Mark Abraham <[email protected]> > wrote: > >> Hi, >> >> That's hard to say. You'd need to do multiple converged simulations at >> each >> set of conditions to know. First, make sure you've made a significant >> observation of the pressure. >> >> Mark >> >> >> On Tue, Nov 4, 2014 at 6:00 PM, Johnny Lu <[email protected]> wrote: >> >> > Hi. >> > >> > If my NVT simulation of a protein in 30k molecules of water has a >> pressure >> > of 11 bar (error 0.5 bar from g_energy), will the dynamics (not >> > distribution of conformations) change enough that the mechanism inferred >> > from this simulation be significantly more unreliable than the mechanism >> > inferred from a 1 bar simulation? (Will the reviewers cut my paper into >> > ribbons?) >> > >> > Thanks again. >> > -- >> > 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 [email protected]. >> > >> -- >> 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 [email protected]. >> > > -- 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 [email protected].
