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!
You are right,But there is another problem: You have not used any -t option in grompp command (doing umbrella step). Since we have set Continuation=yes; Can grompp realize from which .cpt (npt.cpt ) it must use ? And my last question: Do I need to any .cpt file ? (Because I have set Continuation=yes) Thanks in advance On Mon, May 2, 2011 at 3:27 PM, Justin A. Lemkul <[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 | (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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