[gmx-users] Re: gmx-users Digest, Vol 108, Issue 183

Arunima Shilpi writetoash28 at gmail.com
Wed May 1 06:58:16 CEST 2013 

hi alll
 How to generate input.pdb file for umbrella sampling.........





On Wed, May 1, 2013 at 12:42 AM, <gmx-users-request at gromacs.org> wrote:

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> Today's Topics:
>
>    1. Umbrella sampling's equilibration runs (James Starlight)
>    2. Re: Umbrella sampling's equilibration runs (Justin Lemkul)
>    3. Re: help with g_hydorder and g_polystat (Justin Lemkul)
>    4. Aw: [gmx-users] Re: how is the pulling force measured
>       (lloyd riggs)
>    5. Re: Umbrella sampling's equilibration runs (James Starlight)
>    6. stable branch using git (Sikandar Mashayak)
>    7. Re: Aw: [gmx-users] Re: how is the pulling force measured
>       (Justin Lemkul)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 30 Apr 2013 18:58:10 +0400
> From: James Starlight <jmsstarlight at gmail.com>
> Subject: [gmx-users] Umbrella sampling's equilibration runs
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
>         <
> CAALQopwZqTcHgAdfXOhAXqHWeZBB0EDud83inZ379MvDL6Qeuw at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Dear Gromacs users!
>
> I have a question about umbrella sampling simulation based on the Justin's
> tutorial.
>
>
> According to the tutorial after definition of the set of conformers
> extracted from the pulled trajectory I should run N equilibrating
> simulations and N productions runs. In the tutorial I've found that all
> equilibrations run in the NPT ensemble. In my case I have membrane receptor
> for each conformer extracted from the pulling trajectory I want to run 20
> umbrella's simulations with different starting velocities in each case.
> Should I re-equilibrate each conformer in the nvt+npt runs (re-assigning
> velocities in the nvt run) or the velocities might be re-assigned in the
> npt equilibrations ? What the time-prolongation of each equilibrations
> should be for each conformer in case of membrane protein simulation?
>
> Thanks for help
>
> James
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 30 Apr 2013 11:09:08 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Umbrella sampling's equilibration runs
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <517FDE94.2030404 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> On 4/30/13 10:58 AM, James Starlight wrote:
> > Dear Gromacs users!
> >
> > I have a question about umbrella sampling simulation based on the
> Justin's
> > tutorial.
> >
> >
> > According to the tutorial after definition of the set of conformers
> > extracted from the pulled trajectory I should run N equilibrating
> > simulations and N productions runs. In the tutorial I've found that all
> > equilibrations run in the NPT ensemble. In my case I have membrane
> receptor
> > for each conformer extracted from the pulling trajectory I want to run 20
> > umbrella's simulations with different starting velocities in each case.
> > Should I re-equilibrate each conformer in the nvt+npt runs (re-assigning
> > velocities in the nvt run) or the velocities might be re-assigned in the
> > npt equilibrations ? What the time-prolongation of each equilibrations
> > should be for each conformer in case of membrane protein simulation?
> >
>
> If you re-assign velocities to start NPT after NVT, what was the point of
> NVT?
> You destroy the previously established state.  Initialize velocities at the
> start of NVT, then preserve the ensemble information when moving to NPT,
> like
> any other simulation.
>
> The time frame is something you must decide based on your knowledge and
> observations of your system.  There is no definitive answer.
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 30 Apr 2013 11:10:12 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> Subject: Re: [gmx-users] help with g_hydorder and g_polystat
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <517FDED4.6030509 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> On 4/30/13 6:24 AM, Emmanuel, Alaina wrote:
> > Dear All,
> >
> > I'm fairly new to gromacs and having a bit of problem with the
> g_hydorder and g_polystat. Thanks in advanced for your time.
> >
> > For g_hydorder,
> > I get a fatal error when I type the following command:
> > g_hydorder_d -f  file.gro  -s  file.tpr -n waters.ndx -o file1.xpm
> file2.xpm
> > Error:
> > Internal error in pbc_dx, set pbc has nor been called
> > For more information..
> > ----------------------------------------
> >
> > I'm not sure what this means. It seems to be implying that I don't have
> a box around my polymer, but the gro file clearly shows that my box is 4.94
> x 4.94 x 4.94. Any ideas?
> >
>
> What is your setting for the pbc keyword in the .mdp file?
>
> >
> > For g_polystat, I'm a bit worried about the persistence lengths that I
> get for short polymers. With repeat units smaller than 50 these usually
> show "nan" values, that cannot be plotted. From reading the gmx threads
> I've found that Nan stands for "Not a Number", but why do these "nan"
> values appear and how can I prevent it so that I can read in my results?
> >
>
> This could be an underlying problem related to the above interpretation of
> periodicity.  We don't have enough information to say for sure yet.
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> 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: Tue, 30 Apr 2013 18:33:35 +0200 (CEST)
> From: "lloyd riggs" <lloyd.riggs at gmx.ch>
> Subject: Aw: [gmx-users] Re: how is the pulling force measured
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Message-ID:
>
> <trinity-89dd1d93-9768-478a-b2e1-130b33dcb61e-1367339614962 at 3capp-gmx-bs06
> >
>
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> ------------------------------
>
> Message: 5
> Date: Tue, 30 Apr 2013 21:38:17 +0400
> From: James Starlight <jmsstarlight at gmail.com>
> Subject: Re: [gmx-users] Umbrella sampling's equilibration runs
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
>         <
> CAALQopxc7KDEc+JsjmeUZGBL6aJAjfh0ZdZRkdkEguf91qYrjQ at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Justin,
>
>
> could you also tell me
> 1) what difference should be expected from the umbrella sampling run with
> (as I want to do for better coverage) and without (as in your tutorial)
> velocities re-assignment on each umbrella window run ?
>
> 2) On what suggestions should I chose each conformer from pulling
> simulation for each umbrella run? If I have not reasonable kinetiks from
> the pulling simulation could I chose each conformer based on the RMSD from
> the starting structure (in some region- eg in active site) assuming that I
> investigate conformation motions in that region accompanied some functional
> transitions?
>
> Thanks for help,
> James
>
> 2013/4/30 Justin Lemkul <jalemkul at vt.edu>
>
> >
> >
> > On 4/30/13 10:58 AM, James Starlight wrote:
> >
> >> Dear Gromacs users!
> >>
> >> I have a question about umbrella sampling simulation based on the
> Justin's
> >> tutorial.
> >>
> >>
> >> According to the tutorial after definition of the set of conformers
> >> extracted from the pulled trajectory I should run N equilibrating
> >> simulations and N productions runs. In the tutorial I've found that all
> >> equilibrations run in the NPT ensemble. In my case I have membrane
> >> receptor
> >> for each conformer extracted from the pulling trajectory I want to run
> 20
> >> umbrella's simulations with different starting velocities in each case.
> >> Should I re-equilibrate each conformer in the nvt+npt runs (re-assigning
> >> velocities in the nvt run) or the velocities might be re-assigned in the
> >> npt equilibrations ? What the time-prolongation of each equilibrations
> >> should be for each conformer in case of membrane protein simulation?
> >>
> >>
> > If you re-assign velocities to start NPT after NVT, what was the point of
> > NVT? You destroy the previously established state.  Initialize velocities
> > at the start of NVT, then preserve the ensemble information when moving
> to
> > NPT, like any other simulation.
> >
> > The time frame is something you must decide based on your knowledge and
> > observations of your system.  There is no definitive answer.
> >
> > -Justin
> >
> > --
> > ==============================**==========
> >
> > Justin A. Lemkul, Ph.D.
> > Research Scientist
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<
> 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<
> http://lists.gromacs.org/mailman/listinfo/gmx-users>
> > * Please search the archive at http://www.gromacs.org/**
> > Support/Mailing_Lists/Search<
> http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
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>
>
> ------------------------------
>
> Message: 6
> Date: Tue, 30 Apr 2013 14:03:31 -0500
> From: Sikandar Mashayak <symashayak at gmail.com>
> Subject: [gmx-users] stable branch using git
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
>         <CAH+j+HLAsr=
> LoGz_WRAsdnJaaz4tWBXhiDDiCLKPo_SOzFYf7Q at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi
>
> I am following the git tutorial for the novice. It says to check out stable
> version
> one should use "git checkout --track -b release-4-5-patches
> origin/release-4-5-patches"
>
> Is there stable branch for 4.6? If yes, how do get it? I tried replacing
> 4-5 by 4-6 but I get the error:
> fatal: git checkout: updating paths is incompatible with switching
> branches.
> Did you intend to checkout 'origin/release-4-6-patches' which can not be
> resolved as commit?
>
> thanks
> sikandar
>
>
> ------------------------------
>
> Message: 7
> Date: Tue, 30 Apr 2013 15:10:46 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> Subject: Re: Aw: [gmx-users] Re: how is the pulling force measured
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <51801736.2080909 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> On 4/30/13 12:33 PM, lloyd riggs wrote:
> > I appologise, I meant defined at the same time without complaining, not
> just
> > either direction.
>
> A different atom order is interpreted as a different interaction.  In this
> case,
> if both are defined, there is indeed a difference in the improper energy
> term.
> I have a toy test case that shows this.
>
> -Justin
>
> > *Gesendet:* Montag, 29. April 2013 um 22:23 Uhr
> > *Von:* "lloyd riggs" <lloyd.riggs at gmx.ch>
> > *An:* "S. Watkins" <gmx-users at gromacs.org>
> > *Betreff:* Aw: [gmx-users] Re: how is the pulling force measured
> > *Dear All,*
> > *Doing a water/temp energy minimization just for a figure with a large
> molecule
> > that has several connected parts, I ran into a bizzar question.*
> > *So I found its possible by accident to define improper dihedrails
> forwards and
> > backwards without gromacs complaining, such as atom 1 2 3 4 and 4 3 2 1.
>  My
> > question is, if your topology has this, does it affect the calculations
> (angle
> > energy or other)?*
> > *Stephan Watkins*
> >
> >
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> ------------------------------
>
> --
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>
> End of gmx-users Digest, Vol 108, Issue 183
> *******************************************
>
>


-- 

Thanking You with Regards.

Arunima Shilpi

Ph. D Research Scholar(Cancer & Epigenetics)
Department of Life Science
National Institute of Technology
Rourkela
Odisha

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