Sir My query is how to generate input file for umbrella sampling???
On Wed, May 1, 2013 at 6:34 AM, <gmx-users-requ...@gromacs.org> wrote: > [image: Boxbe] <https://www.boxbe.com/overview> This message is eligible > for Automatic Cleanup! (gmx-users-requ...@gromacs.org) Add cleanup > rule<https://www.boxbe.com/popup?url=https%3A%2F%2Fwww.boxbe.com%2Fcleanup%3Ftoken%3DcHAZTM8UoQr3T4gAznTdcpR1dt6MtRPhsWC73mwx2cvLDngyC4%252FdBtiwNGphXYRS7MA5tHT1m24aHTegKXjk%252F66VpGBSLDjW%252BqnlUOWCIUX3exAGj8Kzrmz3O0lhjwCMIo34XQyZfhYqCGbNENOtSnQWV1bs4K1G%26key%3DltcjVdLYz3nK5cIOTwG%252B2ebgI9tvpx1d%252BCwB0cFxnEg%253D&tc_serial=14055619924&tc_rand=1435607005&utm_source=stf&utm_medium=email&utm_campaign=ANNO_CLEANUP_ADD&utm_content=001>| > More > info<http://blog.boxbe.com/general/boxbe-automatic-cleanup?tc_serial=14055619924&tc_rand=1435607005&utm_source=stf&utm_medium=email&utm_campaign=ANNO_CLEANUP_ADD&utm_content=001> > > 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: 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 <jalem...@vt.edu> > Subject: Re: [gmx-users] stable branch using git > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <518063e8.10...@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 <symasha...@gmail.com> > Subject: Re: [gmx-users] stable branch using git > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > < > cah+j+hjynjwwwq7ehre87zrkyeujkn9vh3-kaodfwc9tfof...@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 <jalem...@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@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-requ...@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 <jalem...@vt.edu> > Subject: Re: [gmx-users] stable branch using git > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <518067ad.2060...@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.emman...@warwick.ac.uk> > Subject: RE: [gmx-users] help with g_hydorder and g_polystat > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > < > 780d8855cc75c84bb790b79e4e5de7e7269e8...@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-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on > behalf of Justin Lemkul [jalem...@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@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 > > > > > ------------------------------ > > Message: 5 > Date: Wed, 1 May 2013 01:03:31 +0000 > From: "Emmanuel, Alaina" <a.e.emman...@warwick.ac.uk> > Subject: RE: [gmx-users] help with g_hydorder and g_polystat > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > < > 780d8855cc75c84bb790b79e4e5de7e7269e8...@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-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on > behalf of Justin Lemkul [jalem...@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@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 > > > > > ------------------------------ > > -- > 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 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 -- 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