[gmx-users] Re: gmx-users Digest, Vol 109, Issue 2

Arunima Shilpi writetoash28 at gmail.com
Wed May 1 05:44:53 CEST 2013 

Sir

My query is how to generate input file for umbrella sampling???




On Wed, May 1, 2013 at 6:34 AM, <gmx-users-request at gromacs.org> wrote:

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> Today's Topics:
>
>    1. Re: stable branch using git (Justin Lemkul)
>    2. Re: stable branch using git (Sikandar Mashayak)
>    3. Re: stable branch using git (Justin Lemkul)
>    4. RE: help with g_hydorder and g_polystat (Emmanuel, Alaina)
>    5. RE: help with g_hydorder and g_polystat (Emmanuel, Alaina)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 30 Apr 2013 20:38:00 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> Subject: Re: [gmx-users] stable branch using git
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <518063E8.10605 at vt.edu>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
>
>
> On 4/30/13 8:28 PM, Sikandar Mashayak wrote:
> > Thanks Justin.
> >
> > I replaced release-4-5-patches with release-4-6 while checking out the
> > branch.
> > When I installed it and checked the version string I get VERSION
> > 4.6.2-dev-20130429-d13fc48.
> > Does that mean I got the version which is still under development and not
> > stable and tested?
> > Should I be concerned using it to do a production run?
> >
>
> We generally discourage anyone from doing production work with anything
> that's
> not an official release.  Anything you pull from the git repo is a work in
> progress.  Periodic releases are generated when the code is believed to be
> production-ready.  We do code review and build testing and each patch is as
> reliable as we believe it to be :)
>
> The reference to a "stable branch" is probably a bit misleading, but the
> master
> branch is currently undergoing large-scale changes, leaving it perhaps a
> bit
> more "unstable" than release-4-6.  The release-4-6 branch is the one from
> which
> the development team is producing actual releases.
>
> If you want the latest version, just download the 4.6.1 tarball from the
> Gromacs
> website.  Version 4.6.2 should be out fairly soon, but there are some
> issues
> that are still being cleaned up.
>
> -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: 2
> Date: Tue, 30 Apr 2013 19:50:38 -0500
> From: Sikandar Mashayak <symashayak at gmail.com>
> Subject: Re: [gmx-users] stable branch using git
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
>         <
> CAH+j+HJYNjwwwq7Ehre87zRKyEujkN9vH3-KAodFwc9tfOFmTw at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi Justin
>
> Thanks for explanation. But I am a bit confused because I am new to git.
> When I check out release-4-6 branch, the source code should be the same as
> the one in tarball from Gromacs website, right? When I run git status I get
> # On branch release-4-6
> nothing to commit (working directory clean), I believe that means I have
> the released version of the code.
>
> The reason I am doing this is that I want to have just one directory for
> gromacs with subdirectories for its src, build and binaries. And in future,
> instead of downloading new releases, I want to just pull the changes and
> re-build. Also, I plan to clone the same src directory on my different
> machines, so that I can have the same version on all machines. Hopefully,
> in the future I may start doing some modifications here n there.
>
> Thanks
> Sikandar
>
>
> On Tue, Apr 30, 2013 at 7:38 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 4/30/13 8:28 PM, Sikandar Mashayak wrote:
> >
> >> Thanks Justin.
> >>
> >> I replaced release-4-5-patches with release-4-6 while checking out the
> >> branch.
> >> When I installed it and checked the version string I get VERSION
> >> 4.6.2-dev-20130429-d13fc48.
> >> Does that mean I got the version which is still under development and
> not
> >> stable and tested?
> >> Should I be concerned using it to do a production run?
> >>
> >>
> > We generally discourage anyone from doing production work with anything
> > that's not an official release.  Anything you pull from the git repo is a
> > work in progress.  Periodic releases are generated when the code is
> > believed to be production-ready.  We do code review and build testing and
> > each patch is as reliable as we believe it to be :)
> >
> > The reference to a "stable branch" is probably a bit misleading, but the
> > master branch is currently undergoing large-scale changes, leaving it
> > perhaps a bit more "unstable" than release-4-6.  The release-4-6 branch
> is
> > the one from which the development team is producing actual releases.
> >
> > If you want the latest version, just download the 4.6.1 tarball from the
> > Gromacs website.  Version 4.6.2 should be out fairly soon, but there are
> > some issues that are still being cleaned up.
> >
> >
> > -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!
> > * Please don't post (un)subscribe requests to the list. Use the www
> > interface or send it to gmx-users-request at gromacs.org.
> > * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<
> http://www.gromacs.org/Support/Mailing_Lists>
> >
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 30 Apr 2013 20:54:05 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> Subject: Re: [gmx-users] stable branch using git
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <518067AD.2060207 at vt.edu>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
>
>
> On 4/30/13 8:50 PM, Sikandar Mashayak wrote:
> > Hi Justin
> >
> > Thanks for explanation. But I am a bit confused because I am new to git.
> > When I check out release-4-6 branch, the source code should be the same
> as
> > the one in tarball from Gromacs website, right? When I run git status I
> get
> > # On branch release-4-6
> > nothing to commit (working directory clean), I believe that means I have
> > the released version of the code.
> >
>
> The git version is not the same as the tarball.  The only time the git
> repo and
> source tarball coincide is exactly when a release is produced (i.e. when a
> new
> version is tagged in the git repo).  There have been numerous patches to
> the git
> repo since 4.6.1 was released.
>
> > The reason I am doing this is that I want to have just one directory for
> > gromacs with subdirectories for its src, build and binaries. And in
> future,
> > instead of downloading new releases, I want to just pull the changes and
> > re-build. Also, I plan to clone the same src directory on my different
> > machines, so that I can have the same version on all machines. Hopefully,
> > in the future I may start doing some modifications here n there.
> >
>
> That's what git will allow you to do.
>
> -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: Wed, 1 May 2013 01:00:48 +0000
> From: "Emmanuel, Alaina" <A.E.Emmanuel at warwick.ac.uk>
> Subject: RE: [gmx-users] help with g_hydorder and g_polystat
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
>         <
> 780D8855CC75C84BB790B79E4E5DE7E7269E8129 at DBXPRD0111MB495.eurprd01.prod.exchangelabs.com
> >
>
> Content-Type: text/plain; charset="us-ascii"
>
> Hello Justin,
>
> My mdp file shows that the pbc was set to xyz.
>
>
> Kind Regards,
>
> Alaina
>
> ________________________________________
> From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on
> behalf of Justin Lemkul [jalemkul at vt.edu]
> Sent: 30 April 2013 16:10
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] help with g_hydorder and g_polystat
>
> 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
>
> ========================================
> --
> 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 interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
>
> ------------------------------
>
> Message: 5
> Date: Wed, 1 May 2013 01:03:31 +0000
> From: "Emmanuel, Alaina" <A.E.Emmanuel at warwick.ac.uk>
> Subject: RE: [gmx-users] help with g_hydorder and g_polystat
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
>         <
> 780D8855CC75C84BB790B79E4E5DE7E7269E8139 at DBXPRD0111MB495.eurprd01.prod.exchangelabs.com
> >
>
> Content-Type: text/plain; charset="us-ascii"
>
> Hello Justin,
>
> My mdp file shows that the pbc was set to xyz.
>
>
> Kind Regards,
>
> Alaina
>
> ________________________________________
> From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on
> behalf of Justin Lemkul [jalemkul at vt.edu]
> Sent: 30 April 2013 16:10
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] help with g_hydorder and g_polystat
>
> 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
>
> ========================================
> --
> 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 interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
>
> ------------------------------
>
> --
> 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!
>
> End of gmx-users Digest, Vol 109, Issue 2
> *****************************************
>
>


-- 

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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