Thank you for your detailed axplain I understood completely On Mon, May 2, 2011 at 4:34 PM, Justin A. Lemkul <[email protected]> wrote:
> > > mohsen ramezanpour wrote: > >> Dear Dr.Justin >> >> Thank you for your reply >> My is Protein-ligand,It is have the same conditions as tutorial.I did >> pull ligand in the z direction. >> Actualy I found your note about gen_vel ,but I didn't any about >> Continuation! >> >> > Not that specific keyword, no, but I do address the general principle about > continuing these simulations via this very discussion about gen_vel. > > > You are right,But there is another problem: >> You have not used any -t option in grompp command (doing umbrella >> step). >> >> > Correct. See the discussion on gen_vel that I referenced earlier. > > > Since we have set Continuation=yes; >> Can grompp realize from which .cpt (npt.cpt ) it must use ? >> >> > grompp does not make any choice about what it should use. It takes > whatever input you give it and assembles a run input file. If you're > following my procedure (which may or may not necessarily be applicable in > all cases), then there will NOT be a suitable .cpt file for each starting > configuration. These configurations were generated using SMD, and .cpt > files are not written and saved at every frame so you have a corresponding > one later. > > > And my last question: >> Do I need to any .cpt file ? (Because I have set Continuation=yes) >> >> > Checkpointing and continuation are related, but not identical. The > "continuation" keyword deals with whether or not constraints are solved > before the first integration step. It otherwise has nothing to do with the > thermodynamic state of the system, which is contained in the .cpt file. > > For your system, as I state in the tutorial, you may want to set "gen_vel = > yes" in each window (since there is no prior equilibration, which may be a > problem for some systems, but not the tutorial example). This would > eliminate the need for a .cpt file. > > -Justin > > Thanks in advance >> >> >> >> >> >> On Mon, May 2, 2011 at 3:27 PM, Justin A. Lemkul <[email protected]<mailto: >> [email protected]>> wrote: >> >> >> >> mohsen ramezanpour wrote: >> >> Dear Dr.Justin >> >> Regarding Umbrella Sampling tutorial: >> >> The CONTINUATION option in md_umbrella.mdp is YES, >> and you have noticed : From NPT >> >> I can't understand it's reason correctly! >> >> >> This is a meaningless comment. It was left there from copying and >> pasting files before modifying them. The important part is that >> "continuation = yes" be set to correctly solve the constraints. >> >> >> we run a NPT and then Pulling, then extracted some >> configurations from pull.trr file. >> I think we must continue from pull.cpt not NPT.cpt >> >> I mean : >> grompp -f md_umbrella.mdp ............................. -t >> pull.cpt is more correct than >> >> grompp -f md_umbrella.mdp .............................. -t >> NPT.cpt >> >> am I right? >> >> >> In the case of the tutorial, no. There is not a corresponding .cpt >> file for each configuration generated. If you were to somehow apply >> the same .cpt file for each configuration, almost certainly some of >> the windows would blow up because the initial velocities would cause >> nasty collisions. Note that I discuss the continuation issue, >> proper settings for gen_vel, etc. in the tutorial, step six. >> >> -Justin >> >> >> Thanks in advance for your reply >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- gmx-users mailing list [email protected] >> <mailto:[email protected]> >> >> 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 [email protected] >> <mailto:[email protected]>. >> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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