Hi I want to build my simulation box as tutorial. However I change "vdwradii.dat" file according to the tutorial liquid 2 mix with liquid 1. What should I do?
Thanks Maria On Mon, May 2, 2011 at 5:31 PM, <gmx-users-requ...@gromacs.org> wrote: > Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > gmx-users-requ...@gromacs.org > > You can reach the person managing the list at > gmx-users-ow...@gromacs.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > > 1. Re: Continuation=yes From? (mohsen ramezanpour) > 2. adding an identified number of water molecules (Maria Hamilton) > 3. Re: adding an identified number of water molecules > (Justin A. Lemkul) > 4. adding to liquids in the simulation box: one is in the right > side of the box and the other in the left side (Maria Hamilton) > 5. Re: adding to liquids in the simulation box: one is in the > right side of the box and the other in the left side > (Justin A. Lemkul) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 2 May 2011 16:57:35 +0430 > From: mohsen ramezanpour <ramezanpour.moh...@gmail.com> > Subject: Re: [gmx-users] Continuation=yes From? > To: jalem...@vt.edu, Discussion list for GROMACS users > <gmx-users@gromacs.org> > Message-ID: <banlktink2hpoth3+hhdgtgwyba4m25p...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Thank you for your detailed axplain > I understood completely > > On Mon, May 2, 2011 at 4:34 PM, Justin A. Lemkul <jalem...@vt.edu> 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 <jalem...@vt.edu > <mailto: > >> jalem...@vt.edu>> 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 gmx-users@gromacs.org > >> <mailto: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 > >> <mailto:gmx-users-requ...@gromacs.org>. > >> > >> 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 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 > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20110502/25076a8a/attachment-0001.html > > ------------------------------ > > Message: 2 > Date: Mon, 2 May 2011 17:19:00 +0430 > From: Maria Hamilton <hamilton.mari...@gmail.com> > Subject: [gmx-users] adding an identified number of water molecules > To: gmx-users@gromacs.org > Message-ID: <BANLkTinzfai8AZvEK=l+fxcc7f9-abz...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi all > > If I want to add a simulation box an identified number of water molecules > what should I do? > In manual I see -nmol and -ci in genbox for insert extra molecules but I > don't know for solvent what should I do? > > Thanks alot > > Best Regards > > Maria > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20110502/f486c0c6/attachment-0001.html > > ------------------------------ > > Message: 3 > Date: Mon, 02 May 2011 08:51:51 -0400 > From: "Justin A. Lemkul" <jalem...@vt.edu> > Subject: Re: [gmx-users] adding an identified number of water > molecules > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4dbea8e7.5060...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > Maria Hamilton wrote: > > Hi all > > > > If I want to add a simulation box an identified number of water > > molecules what should I do? > > In manual I see -nmol and -ci in genbox for insert extra molecules but I > > don't know for solvent what should I do? > > > > Please read about the -maxsol option. I think you will find it most > informative. > > -Justin > > > Thanks alot > > > > Best Regards > > > > Maria > > > > -- > ======================================== > > 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 > > ======================================== > > > ------------------------------ > > Message: 4 > Date: Mon, 2 May 2011 17:28:47 +0430 > From: Maria Hamilton <hamilton.mari...@gmail.com> > Subject: [gmx-users] adding to liquids in the simulation box: one is > in the right side of the box and the other in the left side > To: gmx-users@gromacs.org > Message-ID: <banlktims9r4kwssqup_r0wszuvto52n...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi all > > > To do this at first I fill my box using "genbox" with one of the liquids as > solvent: I used -cs and I did not used -cp. > and then I used "genbox" again to add the other liquid in it: first liquid > as a solute and the second one is as solvent. But these two liquids gives > me > a solution. I want to prevent mixing of them. what should I do? > > Thanks alot > > Regards > > Maria > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20110502/0d3ddadb/attachment-0001.html > > ------------------------------ > > Message: 5 > Date: Mon, 02 May 2011 09:00:52 -0400 > From: "Justin A. Lemkul" <jalem...@vt.edu> > Subject: Re: [gmx-users] adding to liquids in the simulation box: one > is in the right side of the box and the other in the left side > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4dbeab04.9080...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > Maria Hamilton wrote: > > Hi all > > > > > > To do this at first I fill my box using "genbox" with one of the liquids > > as solvent: I used -cs and I did not used -cp. > > and then I used "genbox" again to add the other liquid in it: first > > liquid as a solute and the second one is as solvent. But these two > > liquids gives me a solution. I want to prevent mixing of them. what > > should I do? > > > > > http://www.gromacs.org/Documentation/Tutorials?highlight=tutorials#Heterogeneous_Systems > > -Justin > > > Thanks alot > > > > Regards > > > > Maria > > > > -- > ======================================== > > 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 > 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! > > End of gmx-users Digest, Vol 85, Issue 9 > **************************************** >
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