[gmx-users] Re: gmx-users Digest, Vol 85, Issue 9
Maria Hamilton
hamilton.maria39 at gmail.com
Mon May 2 18:09:55 CEST 2011
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-request at gromacs.org> wrote:
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> 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.mohsen at gmail.com>
> Subject: Re: [gmx-users] Continuation=yes From?
> To: jalemkul at vt.edu, Discussion list for GROMACS users
> <gmx-users at gromacs.org>
> Message-ID: <BANLkTink2HpoTh3+HHdgtgWYBa4M25P_SA at 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 <jalemkul at 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 <jalemkul at vt.edu
> <mailto:
> >> jalemkul at 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 at gromacs.org
> >> <mailto:gmx-users at gromacs.org>
> >>
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> Please search the archive at
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> >>
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> >>
> >>
> >>
> > --
> > ========================================
> >
> > 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 at 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
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> ------------------------------
>
> Message: 2
> Date: Mon, 2 May 2011 17:19:00 +0430
> From: Maria Hamilton <hamilton.maria39 at gmail.com>
> Subject: [gmx-users] adding an identified number of water molecules
> To: gmx-users at gromacs.org
> Message-ID: <BANLkTinzfai8AZvEK=L+FXcc7f9-ABZA4A at 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
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> ------------------------------
>
> Message: 3
> Date: Mon, 02 May 2011 08:51:51 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] adding an identified number of water
> molecules
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4DBEA8E7.5060308 at 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.maria39 at 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 at gromacs.org
> Message-ID: <BANLkTims9r4KwSSQup_r0wsZUVTO52NOXw at 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
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> ------------------------------
>
> Message: 5
> Date: Mon, 02 May 2011 09:00:52 -0400
> From: "Justin A. Lemkul" <jalemkul at 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 at gromacs.org>
> Message-ID: <4DBEAB04.9080806 at 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 at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
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>
> End of gmx-users Digest, Vol 85, Issue 9
> ****************************************
>
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