hi alll How to generate input.pdb file for umbrella sampling.........
On Wed, May 1, 2013 at 12:42 AM, <[email protected]> wrote: > [image: Boxbe] <https://www.boxbe.com/overview> This message is eligible > for Automatic Cleanup! 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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 <[email protected]> > Subject: [gmx-users] Umbrella sampling's equilibration runs > To: Discussion list for GROMACS users <[email protected]> > Message-ID: > < > caalqopwzqtchgadfxohaxqhwezbb0edud83inz379mvdl6q...@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 <[email protected]> > Subject: Re: [gmx-users] Umbrella sampling's equilibration runs > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[email protected]> > 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 <[email protected]> > Subject: Re: [gmx-users] help with g_hydorder and g_polystat > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[email protected]> > 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" <[email protected]> > Subject: Aw: [gmx-users] Re: how is the pulling force measured > To: "Discussion list for GROMACS users" <[email protected]> > Message-ID: > > <trinity-89dd1d93-9768-478a-b2e1-130b33dcb61e-1367339614962@3capp-gmx-bs06 > > > > Content-Type: text/plain; charset="us-ascii" > > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20130430/5aa1a7b4/attachment-0001.html > > ------------------------------ > > Message: 5 > Date: Tue, 30 Apr 2013 21:38:17 +0400 > From: James Starlight <[email protected]> > Subject: Re: [gmx-users] Umbrella sampling's equilibration runs > To: Discussion list for GROMACS users <[email protected]> > Message-ID: > < > caalqopxc7kdec+jsjmeuzgbl6ajajfh0zdzrkdkeguf91qy...@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 <[email protected]> > > > > > > > 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 [email protected] > > 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! > > * 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< > http://www.gromacs.org/Support/Mailing_Lists> > > > > > ------------------------------ > > Message: 6 > Date: Tue, 30 Apr 2013 14:03:31 -0500 > From: Sikandar Mashayak <[email protected]> > Subject: [gmx-users] stable branch using git > To: Discussion list for GROMACS users <[email protected]> > Message-ID: > <CAH+j+HLAsr= > [email protected]> > 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 <[email protected]> > Subject: Re: Aw: [gmx-users] Re: how is the pulling force measured > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[email protected]> > 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" <[email protected]> > > *An:* "S. Watkins" <[email protected]> > > *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 > > ======================================== > > > ------------------------------ > > -- > 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! > > 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 -- 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. 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